Re: charm-gui membrane builder

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Sun Sep 08 2013 - 23:52:00 CDT

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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