From: Sunhwan Jo (sunhwan_at_uchicago.edu)
Date: Fri Sep 06 2013 - 15:13:45 CDT
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<mailto: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<mailto: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<mailto: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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