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

**Date:** Thu Sep 12 2013 - 06:24:51 CDT

**Next message:**Michael Shokhen: "How to optimize parameters in command for NAMD CUDA GPU MD calculations?"**Previous message:**Rehan Zafar: "Patching protein with phosphoserine, phosphothreonine and phosphotyrosine patches"**In reply to:**Sunhwan Jo: "Re: charm-gui membrane builder"**Next in thread:**Niklaus Johner: "Re: charm-gui membrane builder"**Reply:**Niklaus Johner: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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:**Michael Shokhen: "How to optimize parameters in command for NAMD CUDA GPU MD calculations?"**Previous message:**Rehan Zafar: "Patching protein with phosphoserine, phosphothreonine and phosphotyrosine patches"**In reply to:**Sunhwan Jo: "Re: charm-gui membrane builder"**Next in thread:**Niklaus Johner: "Re: charm-gui membrane builder"**Reply:**Niklaus Johner: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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