Re: charm-gui membrane builder

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Tue Sep 10 2013 - 11:29:17 CDT

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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