[gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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