On 26/09/2011 10:02 PM, Kavyashree M wrote:
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.
Have you followed the kind of workflow suggested here?
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
I tried visualising it
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?
Yes, one can be visualized, but some preparation with trjconv -ur
compact (as hinted at in trjconv -h) is a good idea.
Mark
Thank you
With regards
Kavya
On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M <[email protected]
<mailto:[email protected]>> wrote:
Thanks.
On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> 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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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