[gmx-users] FW: protein split over boundary

ravi sharma rdsharma_4u at yahoo.com
Fri Apr 1 13:33:35 CEST 2011

Hello anahita,

use pbc in your simulation.



--- On Fri, 1/4/11, anahita <ana_j0000 at yahoo.com> wrote:

From: anahita <ana_j0000 at yahoo.com>
Subject: [gmx-users] FW: protein split over boundary
To: "'Discussion list for GROMACS users'" <gmx-users at gromacs.org>
Date: Friday, 1 April, 2011, 10:53 AM




From: anahita
[mailto:ana_j0000 at yahoo.com] 

Sent: Friday, April 01, 2011 1:13 PM

To: 'gmx-users-request at gromacs.org'

Subject: protein split over boundary 


Dear user, 

Hello, I appreciate if somebody help me. During the
simulation of my protein I didn’t get any error but after 1ns of MD 

my molecule was split over boundary in cubic box. it means
some part of it enter the other side of the box. 

At first,For decreasing the cost of simulation, in
“editconf” command I set the number “d” on 0.9  to decease the box size. I
want to mention that during the calculation my rvdw is 1.4. 

I want to know instead of problem of visualization, the
other things is fine? 

Best regards. 

A. johari 


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