Re: charm-gui membrane builder

From: James Starlight (
Date: Fri Nov 01 2013 - 04:23:07 CDT

Dear Namd users!

I have some question about properly equilibration of the protein inserted
to the membrane made by Charm-gui. This time I've made the whole complex
(not only the membrane) with the protein via charmgui and run all
equilibration steps as well as 10ns unconstraned simulation.
During analysis of this 10ns (all simulation parameters have been used from
the last equilibration step produced by Charmgui) I observed slight
decrease in X-Y and increase in Z dimensions of the PBC as well as motion
of the protein as the whole (!!!) in the x-y plane of the membrane
(analysis of the RMSD and the visual SS inspection provides me hight
increase in RMSD (up to 10A) during first 2ns when such 2D diffusion have
been detected. On other hand detailed analysis indicated low RMSD per each
residue (up to 2 A in case of loops) and preserving of the helical
structure of my protein during whole run. I'm not sure if this simulation
was OK because I've never seen such motion in X-Y plane (previously making
long simulation in Gromacs with Langevins dynamics and Parinello's
barostat). If it possible I can upload picture of my system at the end of
the simulation for better visual inspection


2013/9/6 James Starlight <>

> 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
> Equilibration Step1:step6.1_equilibration.inp<> Equilibration
> Step2:step6.2_equilibration.inp<> Equilibration
> Step3:step6.3_equilibration.inp<> Equilibration
> Step4:step6.4_equilibration.inp<> Equilibration
> Step5:step6.5_equilibration.inp<> Equilibration
> Step6:step6.6_equilibration.inp<>
> but how I can create psf from that data?
> James

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