[gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane

Shima Arasteh shima_arasteh2001 at yahoo.com
Thu Oct 11 13:27:43 CEST 2012

This is a sample of energy minimization, solvation and ion neutralization in my own system ( protein in POPC):

Steepest Descents converged to Fmax < 100 in 18240 steps
Potential Energy  = -1.0357691e+06
Maximum force     =  8.0741402e+01 on atom 4716
Norm of force     =  3.1694601e+00

I think it seems sensible, however I am not sure.


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, October 11, 2012 2:21 PM
Subject: Re: [gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane

On 10/11/12 5:57 AM, Shima Arasteh wrote:
> I visualized the last output mdrun of KALP15-DPPC simulation, the secondary structure of protein is complete and it seems OK. Can I trust on it and not care about the visualization of system after inflategro?

That's probably a reasonable conclusion.  Sometimes visualization can be misleading.  What you should trust the most is the outcome of the EM during shrinking of InflateGRO and whether it generates sensible forces.


-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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