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
========================================
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