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

Shima Arasteh shima_arasteh2001 at yahoo.com
Thu Oct 11 13:39:54 CEST 2012


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, October 11, 2012 3:00 PM
Subject: Re: [gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane

On 10/11/12 7:27 AM, Shima Arasteh wrote:
> 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.

Perfectly reasonable.  You achieved an Fmax below the desired value and its 
magnitude makes sense given the size of the system.



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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