From: James Starlight (jmsstarlight_at_gmail.com)
Date: Fri Sep 06 2013 - 11:24:56 CDT
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>
> 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.
> Sent from my iPhone
> On Sep 6, 2013, at 6:35 AM, "James Starlight" <jmsstarlight_at_gmail.com>
> Dear Namd Users!
> I've already seen similar topic previously but didn't find any possible
> How I could use charm gui outputs to generate namd psf file of the
> generated membrane ? In my case charm gui generated 6 files
> 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?
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