[gmx-users] weird mdrun...using gromacs 3.3.3

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 8 19:18:54 CEST 2009

Naga Rajesh Tummala wrote:
> Dear Justin,
> The initial configuration for this simulation is the configuration 
> obtained from 10 ns of simulation. The only thing that is changed is 
> that I now consider a nanotube as a single rigid body connected by 
> bonds, so that I can make the nanotube move along the x-direction as a 
> whole.
> I did write a small FORTRAN code to check for atomic overlap (especially 
> between FMN and CNT, FMN-CMT , SOD-CNT, SOD-CMT). I could not find any 
> atomic pair less than 0.3 nm.

Can you post the relevant .mdp file(s)?  Are you preserving velocity information 
from the previous trajectory, or generating new velocities?  Are any of the 
species in your system constrained?


> Thanks
> Rajesh
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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