**From:** James Starlight (*jmsstarlight_at_gmail.com*)

**Date:** Fri Sep 13 2013 - 02:06:07 CDT

**Next message:**James Starlight: "Re: First meeting with NAMD"**Previous message:**Niklaus Johner: "Re: charm-gui membrane builder"**Maybe in reply to:**Sunhwan Jo: "Re: charm-gui membrane builder"**Next in thread:**Niklaus Johner: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Some questions about system constructions.

I've successfully equilibrate my system consisted of the neutralized

bilayer. But after protein insertion (this protein has total charge +1)

some charged lipids was removed. Then I remove all initial ions placed by

charm-gui and make new ionization.

after this step ionization I've obtained

Info) Opened coordinate file ionized.pdb for writing.

Info) Finished with coordinate file ionized.pdb.

Autoionize) System net charge after adding ions: -0.4259657543152571e.

How It could be fixed ?

James

2013/9/13 James Starlight <jmsstarlight_at_gmail.com>

*> Hi,
*

*>
*

*> sorry I can browse mailing list from my mail box only and there are no
*

*> search buttons available here :D
*

*>
*

*> In any case I'll be thankful for any helpful links to previous discussions.
*

*>
*

*> James
*

*>
*

*>
*

*> 2013/9/12 Niklaus Johner <niki.johner_at_gmail.com>
*

*>
*

*>> Hi,
*

*>>
*

*>> Before posting to the mailing list you should search previous threads
*

*>> (there is one exactly on this and it took me 1second to find it) and google
*

*>> what you're looking for. Moreover this is not really a namd question AND I
*

*>> have already answered you on this.
*

*>>
*

*>> At some point yo'll have to try to work some things out by yourself.
*

*>> There are tons of available tcl scripts for vmd that you can use as a basis
*

*>> for doing your analysis, or you can use some other analysis tools such as
*

*>> the gromacs tools or so.
*

*>>
*

*>> N.
*

*>>
*

*>> Niklaus Johner
*

*>> Weill Cornell Medical College
*

*>> Harel Weinstein Lab
*

*>> Department of Physiology and Biophysics
*

*>> 1300 York Avenue, Room D-501
*

*>> New York, NY 10065
*

*>>
*

*>>
*

*>>
*

*>> On Sep 12, 2013, at 7:24 AM, James Starlight wrote:
*

*>>
*

*>> Sunhwan,
*

*>>
*

*>> thanks again for suggestions! It seems that problem was in the absence of
*

*>> the counter-ions. I've forgot that I used charged lipids ;o
*

*>>
*

*>> Could you tell me what VMD extensions could I use for analysis of my
*

*>> bilayer? ( e.g I want to verify results of the simulation with experimental
*

*>> data like area per lipid for instance)
*

*>>
*

*>> James
*

*>>
*

*>>
*

*>> 2013/9/12 Sunhwan Jo <sunhwan_at_uchicago.edu>
*

*>>
*

*>>> James,
*

*>>>
*

*>>> I do not encounter problems equilibrating bilayer in general. You
*

*>>> should be careful when very high concentration of cholesterol or highly
*

*>>> irregular shape of protein is used, because lipid tails could penetrate the
*

*>>> protein surface or cholesterol ring system.
*

*>>>
*

*>>> If you read your input, step6.1 and step6.2 perform NVT simulation,
*

*>>> and step6.3 and later perform NPT simulations. Thus, your simulation system
*

*>>> can expand during step6.3. So, no wonder you could workaround this problem
*

*>>> by using "useConstantArea" option.
*

*>>>
*

*>>> To me, the only remaining question would be whether the expansion is
*

*>>> expected or not. I realized you are referring to a new system below. I have
*

*>>> downloaded your system and it seems the system is not properly neutralized
*

*>>> and have total charge of -160e. I never have run a system that is not
*

*>>> properly neutralized, so I'm not sure if the problem you having is the
*

*>>> consequence of that or not.
*

*>>>
*

*>>> Is there any reason you have decided not to include ions? Perhaps NAMD
*

*>>> can takes care of non-neutral simulation system, but those charges (-80e in
*

*>>> each leaflet) repel each other and make your system to expand rapidly.
*

*>>>
*

*>>> Best,
*

*>>> Sunhwan
*

*>>>
*

*>>> On Sep 11, 2013, at 3:15 PM, James Starlight <jmsstarlight_at_gmail.com>
*

*>>> wrote:
*

*>>>
*

*>>> Sunhwan,
*

*>>>
*

*>>> have you any problems with my bilayer during equilibration? Briefly
*

*>>> using charm-gui input files on the 6.3 stage my bilayer rapidly expanded in
*

*>>> the X plane and shrunk in the Z plane and during 6/4 stage the simulation
*

*>>> have been crushed with PBC dimensions error.
*

*>>>
*

*>>> This particularly have been fixed by inclusion in the conf file
*

*>>> useConstantArea option
*

*>>> instead of useConstantRatio. All those simulations have been performed
*

*>>> with latest NAMD on CUDA.
*

*>>>
*

*>>> James
*

*>>>
*

*>>>
*

*>>> 2013/9/11 Sunhwan Jo <sunhwan_at_uchicago.edu>
*

*>>>
*

*>>>> James,
*

*>>>>
*

*>>>> I'm the main authors of CHARMM-GUI membrane builder and our NAMD
*

*>>>> input files has been throughly tested for NAMD 2.8 and above. One of my
*

*>>>> colleague even tested with your simulation system using NAMD 2.9 (CPU), so
*

*>>>> I'm not certain why you having such problem. Let me know if there is
*

*>>>> anything that we can do to help.
*

*>>>>
*

*>>>> Thanks,
*

*>>>> Sunhwan
*

*>>>>
*

*>>>>
*

*>>>> On Sep 11, 2013, at 12:20 PM, James Starlight <jmsstarlight_at_gmail.com>
*

*>>>> wrote:
*

*>>>>
*

*>>>> My problem have been solved via adding below term to the conf file
*

*>>>>
*

*>>>> useConstantArea yes ;
*

*>>>>
*

*>>>> instead of
*

*>>>> useConstantRatio yes ; # which was presented on the default charm-gui
*

*>>>> conf file.
*

*>>>>
*

*>>>> I'm not sure if this is possible to make such changes to the NON
*

*>>>> equilibrated bilayers but this prevent crash with PBC error
*

*>>>>
*

*>>>>
*

*>>>> also could my problem be solved providing softer coupling to the
*

*>>>> pressure bath increasing below two params ?
*

*>>>>
*

*>>>> langevinPistonPeriod 200.0
*

*>>>> langevinPistonDecay 50.0
*

*>>>>
*

*>>>> Finally does anybody knows some pre-equlibrated bilayers with
*

*>>>> suitable namd inputs ?
*

*>>>>
*

*>>>> James
*

*>>>>
*

*>>>>
*

*>>>> 2013/9/10 James Starlight <jmsstarlight_at_gmail.com>
*

*>>>>
*

*>>>>> Thanks again for suggestions!
*

*>>>>>
*

*>>>>> That problem has been solved performing minimization as the separate
*

*>>>>> step on the CPU-only.
*

*>>>>>
*

*>>>>> The new problem have been arrisen when I add the barostat to my
*

*>>>>> system on the 6.3 step
*

*>>>>>
*

*>>>>>
*

*>>>>> # constant pressure
*

*>>>>> langevinPiston on
*

*>>>>> langevinPistonTarget 1.01325
*

*>>>>> langevinPistonPeriod 200.0
*

*>>>>> langevinPistonDecay 50.0
*

*>>>>> langevinPistonTemp $temp
*

*>>>>>
*

*>>>>> from the beginning of this step the bi-layer have been increased in
*

*>>>>> XY plane rapidly and shrunk in the Z plane ( this simulation have been
*

*>>>>> performed with GPU). How this issue could be solved ?
*

*>>>>>
*

*>>>>>
*

*>>>>> 2013/9/9 James Starlight <jmsstarlight_at_gmail.com>
*

*>>>>>
*

*>>>>>> I've just tried to make such minimization + equilibration in the
*

*>>>>>> different steps
*

*>>>>>> with that system
*

*>>>>>> http://www.charmm-gui.org/?doc=input/membrane_only&time=1378378701
*

*>>>>>>
*

*>>>>>> but unfortunately after minimization my system have been crashed
*

*>>>>>> during beginning of the production run (
*

*>>>>>>
*

*>>>>>> James
*

*>>>>>>
*

*>>>>>>
*

*>>>>>> 2013/9/9 Cesar Millan <pachequin_at_gmail.com>
*

*>>>>>>
*

*>>>>>>> Hi,
*

*>>>>>>>
*

*>>>>>>> I really don't know, I just made that changes and it worked.
*

*>>>>>>>
*

*>>>>>>> Best regards.
*

*>>>>>>>
*

*>>>>>>> Cesar
*

*>>>>>>>
*

*>>>>>>>
*

*>>>>>>> ############################
*

*>>>>>>> César Millán Pacheco
*

*>>>>>>> Facultad de Ciencias
*

*>>>>>>> Universidad Autonoma del Estado de Morelos
*

*>>>>>>> Tel: 777 3297020
*

*>>>>>>> Fax: 777 3207040
*

*>>>>>>> email: cmp_at_uaem.mx
*

*>>>>>>> pachequin_at_gmail.com
*

*>>>>>>>
*

*>>>>>>>
*

*>>>>>>>
*

*>>>>>>> On Sun, Sep 8, 2013 at 11:52 PM, James Starlight <
*

*>>>>>>> jmsstarlight_at_gmail.com> wrote:
*

*>>>>>>>
*

*>>>>>>>> Cesar, thank you for suggestion!
*

*>>>>>>>>
*

*>>>>>>>> Should I make any extra changes to the minim.inp file (made based
*

*>>>>>>>> on the step6.1 template )?
*

*>>>>>>>>
*

*>>>>>>>> Is it possible to turned-off GPU-regime during some equilibration
*

*>>>>>>>> step ? I'd like to check if the possible soursse of such errors in GPU.
*

*>>>>>>>>
*

*>>>>>>>> James
*

*>>>>>>>>
*

*>>>>>>>>
*

*>>>>>>>> 2013/9/9 Cesar Millan <pachequin_at_gmail.com>
*

*>>>>>>>>
*

*>>>>>>>>> I dont turn off the gpu regime. I just create 3 new files using
*

*>>>>>>>>> charmm-gui input files as templates. On step6.1.equ...inp, I separate it on
*

*>>>>>>>>> two files step6.1.equilibration_min.inp and step6.1.equilibration_din.inp.
*

*>>>>>>>>> After that on step6.1...min.inp i delete the "run ...." line and on
*

*>>>>>>>>> step6.1...din.inp I delete those lines that implies a minimization process.
*

*>>>>>>>>> You have to check that the names of step6.1....min.inp are the input names
*

*>>>>>>>>> for step6.1....din.inp.
*

*>>>>>>>>>
*

*>>>>>>>>> Hope this helps.
*

*>>>>>>>>>
*

*>>>>>>>>> Cesar
*

*>>>>>>>>>
*

*>>>>>>>>>
*

*>>>>>>>>>
*

*>>>>>>>>> ############################
*

*>>>>>>>>> César Millán Pacheco
*

*>>>>>>>>> Facultad de Ciencias
*

*>>>>>>>>> Universidad Autonoma del Estado de Morelos
*

*>>>>>>>>> Tel: 777 3297020
*

*>>>>>>>>> Fax: 777 3207040
*

*>>>>>>>>> email: cmp_at_uaem.mx
*

*>>>>>>>>> pachequin_at_gmail.com
*

*>>>>>>>>>
*

*>>>>>>>>>
*

*>>>>>>>>>
*

*>>>>>>>>> On Sun, Sep 8, 2013 at 12:04 PM, James Starlight <
*

*>>>>>>>>> jmsstarlight_at_gmail.com> wrote:
*

*>>>>>>>>>
*

*>>>>>>>>>> Cesar,
*

*>>>>>>>>>>
*

*>>>>>>>>>> could you tell me how should I run my simulation in gpu turned
*

*>>>>>>>>>> off regime ? I've not found this in man (
*

*>>>>>>>>>>
*

*>>>>>>>>>> James
*

*>>>>>>>>>>
*

*>>>>>>>>>>
*

*>>>>>>>>>> 2013/9/8 Cesar Millan <pachequin_at_gmail.com>
*

*>>>>>>>>>>
*

*>>>>>>>>>>> Hi, I've done this kind of systems before on GPUs. You have to
*

*>>>>>>>>>>> separate minimization and dynamics.
*

*>>>>>>>>>>> Run the minimization process with the NAMD CPU version and the
*

*>>>>>>>>>>> dynamics with the NAMD GPU version.
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> best regards.
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> Cesar
*

*>>>>>>>>>>>
*

*>>>>>>>>>>>
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> ############################
*

*>>>>>>>>>>> César Millán Pacheco
*

*>>>>>>>>>>> Facultad de Ciencias
*

*>>>>>>>>>>> Universidad Autonoma del Estado de Morelos
*

*>>>>>>>>>>> Tel: 777 3297020
*

*>>>>>>>>>>> Fax: 777 3207040
*

*>>>>>>>>>>> email: cmp_at_uaem.mx
*

*>>>>>>>>>>> pachequin_at_gmail.com
*

*>>>>>>>>>>>
*

*>>>>>>>>>>>
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> On Sun, Sep 8, 2013 at 11:44 AM, James Starlight <
*

*>>>>>>>>>>> jmsstarlight_at_gmail.com> wrote:
*

*>>>>>>>>>>>
*

*>>>>>>>>>>>> It seems that problem was not in cholesterol
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> E.g I've tried to equilibration this simplest system
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> http://www.charmm-gui.org/?doc=input/membrane_only&time=1378628752
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> and after long minimization I've obtained error
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 30000
*

*>>>>>>>>>>>> WRITING COORDINATES TO DCD FILE AT STEP 30000
*

*>>>>>>>>>>>> WRITING COORDINATES TO RESTART FILE AT STEP 30000
*

*>>>>>>>>>>>> FINISHED WRITING RESTART COORDINATES
*

*>>>>>>>>>>>> WRITING VELOCITIES TO RESTART FILE AT STEP 30000
*

*>>>>>>>>>>>> FINISHED WRITING RESTART VELOCITIES
*

*>>>>>>>>>>>> TCL: Setting parameter numsteps to 90000000
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> TCL: Original numsteps 90000000 will be ignored.
*

*>>>>>>>>>>>> TCL: Running for 25000 steps
*

*>>>>>>>>>>>> REASSIGNING VELOCITIES AT STEP 30000 TO 310 KELVIN.
*

*>>>>>>>>>>>> colvars: Writing the state file
*

*>>>>>>>>>>>> "step6.1_equilibration.restart.colvars.state".
*

*>>>>>>>>>>>> colvars: Synchronizing (emptying the buffer of) trajectory file
*

*>>>>>>>>>>>> "step6.1_equilibration.colvars.traj".
*

*>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 14039!
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 8959!
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 66!
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 15321!
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 13670!
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 9380!
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 5019!
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 11279!
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 7260!
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 18406!
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>> ERROR: Exiting prematurely; see error messages above.
*

*>>>>>>>>>>>> ====================================================
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> I'm not sure if it possible to run simulation purely with the
*

*>>>>>>>>>>>> CPU (turned off GPU) on my machine
*

*>>>>>>>>>>>> Typically I run simulation with GPU by means of
*

*>>>>>>>>>>>> namd2 +idlepoll +p4 +devices 0 ./step6.2_equilibration.inp
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> May be some extra parameters should be provided in the conf
*

*>>>>>>>>>>>> file when I simulate with GPU? E.g I suppose that some addition should be
*

*>>>>>>>>>>>> added to the PBC as well as PME options.
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> James
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>> 2013/9/8 Sunhwan Jo <sunhwan_at_uchicago.edu>
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>>> James,
*

*>>>>>>>>>>>>>
*

*>>>>>>>>>>>>> Can you try with CPU version of NAMD?
*

*>>>>>>>>>>>>>
*

*>>>>>>>>>>>>> Sunhwan
*

*>>>>>>>>>>>>>
*

*>>>>>>>>>>>>> Sent from my iPhone
*

*>>>>>>>>>>>>>
*

*>>>>>>>>>>>>> On Sep 8, 2013, at 12:04 AM, "James Starlight" <
*

*>>>>>>>>>>>>> jmsstarlight_at_gmail.com> wrote:
*

*>>>>>>>>>>>>>
*

*>>>>>>>>>>>>> Emilia,
*

*>>>>>>>>>>>>>
*

*>>>>>>>>>>>>> I've already tried to increase minimization step number but
*

*>>>>>>>>>>>>> result was the same.
*

*>>>>>>>>>>>>>
*

*>>>>>>>>>>>>> Briefly I've just tried to minimize my system (for example
*

*>>>>>>>>>>>>> the system which I've shown or also I have the same system with reduced
*

*>>>>>>>>>>>>> water layers) during equilibration step6.1 with namd 2.9(gpu-simulation
*

*>>>>>>>>>>>>> regime). By the way what other options of the minimization can I change
*

*>>>>>>>>>>>>> besides step number as well as integrator timestep (e.g can I vary gradient
*

*>>>>>>>>>>>>> degree or minimization algorithm )?
*

*>>>>>>>>>>>>>
*

*>>>>>>>>>>>>> James
*

*>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>
*

*>>>>>>>>>>>>> 2013/9/7 Emilia Wu <emilia.l.wu_at_gmail.com>
*

*>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>> You can minimize more steps before dynamics starts. The
*

*>>>>>>>>>>>>>> default number in the input might be too small for your big system.
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>> Emilia
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>> On Sep 7, 2013, at 4:04 AM, James Starlight wrote:
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>> Emillia,
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>> I've tried to launch simulation from the files produced by
*

*>>>>>>>>>>>>>> charm-gui but simulation have crashed on the beginning of the first
*

*>>>>>>>>>>>>>> equilibration step after long minimization with the error
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>> TCL: Original numsteps 90000000 will be ignored.
*

*>>>>>>>>>>>>>> TCL: Running for 25000 steps
*

*>>>>>>>>>>>>>> REASSIGNING VELOCITIES AT STEP 0 TO 303.15 KELVIN.
*

*>>>>>>>>>>>>>> Pe 2 has 36 local and 36 remote patches and 972 local and 972
*

*>>>>>>>>>>>>>> remote computes.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4962!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 5678!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 2288!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 5370!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3089!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3759!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 20746!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 14993!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 2681!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4697!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1669!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1634!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4731!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 2191!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 6835!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 942!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 11615!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3217!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 7862!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1920!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 723!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1030!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 2733!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 262!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 336!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1259!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1201!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3491!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 5287!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 145!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 6863!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 7462!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1811!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 397!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 854!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1453!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1792!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 8914!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 10618!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3135!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 7368!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 13152!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 6171!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 8533!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 21871!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 9658!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1715!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 2824!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 12533!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 8990!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 751!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4164!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 6875!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 175!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1156!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 455!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 9569!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1535!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 435!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 7012!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 5552!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3525!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3266!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 256!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 6265!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3155!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 2209!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 24!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4392!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4495!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4751!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 552!
*

*>>>>>>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>>>>>>> ERROR: Exiting prematurely; see error messages above.
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>> It looks like my system have not been equilibrated properly
*

*>>>>>>>>>>>>>> and I have the same eror only in case of big systems. How I could fix it?
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>> James
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>> 2013/9/7 Sunhwan Jo <sunhwan_at_uchicago.edu>
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>> James,
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>> My labmate has downloaded your files and ran step6.1 input
*

*>>>>>>>>>>>>>>> using NAMD_2.9_Linux-x86_64-TCP/namd2. We didn't find any problems with the
*

*>>>>>>>>>>>>>>> minimization and it was working well in our test.
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>> Sunhwan
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>> On Sep 6, 2013, at 11:24 AM, James Starlight <
*

*>>>>>>>>>>>>>>> jmsstarlight_at_gmail.com> wrote:
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>> Dear all !
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>> Thanks for suggestions!
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>> I've mentioned in the adjacent topic the problem of
*

*>>>>>>>>>>>>>>> minimization for the system consisted of many lipids + water (produced by
*

*>>>>>>>>>>>>>>> charm_gui).
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>> Briefly when I try to minimize clashes in big systems (
*

*>>>>>>>>>>>>>>> many lipids + solvent) the minimization didt work ( its looks like all
*

*>>>>>>>>>>>>>>> atoms were frozen during whole minimization trajectory so the clashes didnt
*

*>>>>>>>>>>>>>>> resolved ).
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>> When I try to minimize the same system without water (only
*

*>>>>>>>>>>>>>>> lipids)- there were no problem at all (the lipid tales constantly moves
*

*>>>>>>>>>>>>>>> during minimization resolving clashes between them) .
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>> To fix this problem I've tried to add FIX ATOMS to all water
*

*>>>>>>>>>>>>>>> according to tutorial but the problem have not been solved in case of big
*

*>>>>>>>>>>>>>>> systems. How I should minimize it ?
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>> 2013/9/6 Sunhwan Jo <sunhwan_at_uchicago.edu>
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>> James
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>> CHARMM-GUI generates step_assembly.xplor.psf, which can
*

*>>>>>>>>>>>>>>>> be used in NAMD. Perhaps this file is not displayed on webpage. You can
*

*>>>>>>>>>>>>>>>> download every file generated by GUI by using "download .tgz" link on the
*

*>>>>>>>>>>>>>>>> upper right corner of the webpage.
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>> Sunhwan
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>> Sent from my iPhone
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>> On Sep 6, 2013, at 6:35 AM, "James Starlight" <
*

*>>>>>>>>>>>>>>>> jmsstarlight_at_gmail.com> wrote:
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>> Dear Namd Users!
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>> I've already seen similar topic previously but didn't find
*

*>>>>>>>>>>>>>>>> any possible solution.
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>> How I could use charm gui outputs to generate namd psf
*

*>>>>>>>>>>>>>>>> file of the generated membrane ? In my case charm gui generated 6 files
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>> http://www.charmm-gui.org/?doc=input/membrane_only&time=1378378701
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>> Equilibration Step1: step6.1_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.1_equilibration.inp> Equilibration
*

*>>>>>>>>>>>>>>>> Step2: step6.2_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.2_equilibration.inp> Equilibration
*

*>>>>>>>>>>>>>>>> Step3: step6.3_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.3_equilibration.inp> Equilibration
*

*>>>>>>>>>>>>>>>> Step4: step6.4_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.4_equilibration.inp> Equilibration
*

*>>>>>>>>>>>>>>>> Step5: step6.5_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.5_equilibration.inp> Equilibration
*

*>>>>>>>>>>>>>>>> Step6: step6.6_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.6_equilibration.inp>
*

*>>>>>>>>>>>>>>>> but how I can create psf from that data?
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>> James
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>>
*

*>>>>>>>>>>>>>
*

*>>>>>>>>>>>>
*

*>>>>>>>>>>>
*

*>>>>>>>>>>
*

*>>>>>>>>>
*

*>>>>>>>>
*

*>>>>>>>
*

*>>>>>>
*

*>>>>>
*

*>>>>
*

*>>>>
*

*>>>
*

*>>>
*

*>>
*

*>>
*

*>
*

**Next message:**James Starlight: "Re: First meeting with NAMD"**Previous message:**Niklaus Johner: "Re: charm-gui membrane builder"**Maybe in reply to:**Sunhwan Jo: "Re: charm-gui membrane builder"**Next in thread:**Niklaus Johner: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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