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

[Shima Arasteh]

Thanks.
 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
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

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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