On 8/16/13 5:09 PM, HANNIBAL LECTER wrote:
Hi,
I am trying to simulate nanotube (1156) with protein and water and I am
using Tcoupl = system using sd integrator in gromacs.
Since I am position restraining the nanotube, I would expect that the
restrained CNT degrees of freedom are accounted for while calculating the
system temperatures using g_traj. However, for a ref-t = 300K the system
temperature is reported to be ~292K. As a control, I performed simulations
with
Tcoupl=CNT Protein SOL and in that case the temperatures from g_energy are
reported thus CNT~157K Protein~296K and Solvent ~300K. It clearly shows
that the CNT constrained dof are not accounted for correctly. Is that the
case or am I missing something?
Constraints are restraints are different. If you are using constraints on any
bonds in your system, the value from g_traj is wrong and you have to manually
correct for it.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
