On 8/17/13 12:10 AM, HANNIBAL LECTER wrote:
Thanks. Is there any way to position restraint a part of the system while
keeping all bonds flexible?
Sure. Apply position restraints as normal and set "constraints = none" in the
.mdp file. This will affect your choice of dt, though, and SETTLE is still
applied to water molecules.
-Justin
On Fri, Aug 16, 2013 at 5:24 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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
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Justin A. Lemkul, Ph.D.
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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
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