Re: charm-gui membrane builder

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Fri Sep 06 2013 - 15:03:41 CDT

some extra question about Charm-gui output archive.

In that archive I've found 7 conf (inp) files suitable for step-by-step
equilibration but I've not understood where I can find script which
integrate all process and define all variables listed in each conf file.
I'll be thankful if someone provide me with that information or with simple
example.

James

2013/9/6 James Starlight <jmsstarlight_at_gmail.com>

> 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
>>
>>
>

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:37 CST