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

[Justin A. Lemkul]

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?

-Justin

> Thanks
> Rajesh
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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