Re: charm-gui membrane builder

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Thu Sep 12 2013 - 06:24:51 CDT

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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>
>

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