[gmx-users] Dimer simulation problem

Kavyashree M hmkvsri at gmail.com
Mon Sep 26 14:02:29 CEST 2011

Hello again,

I centered it and then did the calculation again for minimum image distance
but still it showed the same graph as without centering. I tried visualising
using vmd but could not see any such clashes. since I am new to vmd
I do not know whether it is possible to calculate such clashes if at all
in vmd? I am using dodecahedron box. can it be visualised as it is in vmd?

Thank you
With regards

On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M <hmkvsri at gmail.com> wrote:

> Thanks.
> On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> Kavyashree M wrote:
>>> Dear users,
>>> I was trying to simulate a protein dimer covalently bond with
>>> a disulphide bond (230+230 aa long). I used usual protocol
>>> as used for simulation of a monomeric protein, using gromacs-
>>> 4.5.3, dodecahedron box, tip4p water model and protein to
>>> box distance of 1 (-d in editconf). In the middle of the simulation
>>> when i checked for minimum image violation there was huge
>>> clashes. I am extremely sorry I have been asking regarding this
>>> many times but in this it is a dimer and I am not sure what mistake
>>> I have done because this happened while simulating another dimer
>>> also though not sever. Hence I seek some guidance from this
>>> community regarding the problem. I attach the graph herewith.
>>> Kindly help. Let me know if I need to give any other information.
>> Please see my post from yesterday for a more detailed reply to this exact
>> same type of question.  I am beginning to suspect there's a problem with
>> g_mindist, but I have no solid evidence for that claim, just a hunch.  It
>> looks like your protein crosses a periodic boundary and that messes up the
>> calculation.  Please center the protein in the box with trjconv -center and
>> re-analyze to see if there are any differences.
>> -Justin
>> --
>> ==============================**==========
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> ==============================**==========
>> --
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