[gmx-users] drug-enzyme simulation.

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 29 03:07:55 CEST 2009

Neha Gandhi wrote:
> Hi List,
> 1) I m running a drug -enzyme simulation. I ran 62 ps of simulated
> annealing followed by  production runs of 5ns usng NPT and PBC and
> PME.. After 5ns, the protein moves far away from the ligand.  I
> checked the 4ns gro files, the ligand and protein are bound together,
> but its only that 5ns gives issues.
> 2) I ran another similar but smaller system and the complex is stable
> even after 8ns.
> What went wrong with the simulations in case 1? Is there a way to fix
> this problem?

Did the protein and/or ligand cross a periodic boundary?  If so, trjconv can 
"fix" this visualization artifact.


> Your help is much appreciated.
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list