[gmx-users] Dimer simulation

Kavyashree M hmkvsri at gmail.com
Sat Sep 17 16:43:18 CEST 2011

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.

Thanking you
With Regards
M. Kavyashree
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110917/f27ad8b2/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: therm.png
Type: image/png
Size: 17577 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110917/f27ad8b2/attachment.png>

More information about the gromacs.org_gmx-users mailing list