[gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

Justin Lemkul jalemkul at vt.edu
Fri Jul 11 02:00:22 CEST 2014

On 7/10/14, 7:09 PM, Rasoul Nasiri wrote:
> Because
> 1- Estimation of T for different sub-systems say phases of gas, interface
> and liquid.
> Can be obtained with g_energy?

No, not unless they are assigned as separate tc-grps in the .mdp file, but then 
(1) you shouldn't be designing something affecting the physics purely based on 
what you hope to analyze and (2) you then already know the outcome.

This is actually what g_traj can do; like I said, you just have to account for 

> 2- My trajectory is not constrain one as it has been recorded using
> reactive FF.
> I need to estimate T with converted trajectory (reaxff---->gro).

Converted trajectory?  Your first post suggested the run was done with Gromacs 
(being that you had .tpr and .edr files).  The outcomes you posted agree 
perfectly with constrained molecules, but without more details on what you're 
actually doing, I'm not going to hazard a guess.  Recall that even if you set 
"constraints = none," SETTLE is still applied to water molecules unless you use 
-DFLEXIBLE (which you shouldn't for most normal purposes).



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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