[gmx-users] inconsistency in obtained temperature values by traj and g_energy tools
nasiri1355 at gmail.com
Fri Jul 11 03:30:59 CEST 2014
On Fri, Jul 11, 2014 at 12:58 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 7/10/14, 7:09 PM, Rasoul Nasiri wrote:
>> 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,
as sub-systems are changing during the simulation in terms of number of
atoms in a non-equilibrium situation, I don't think g_energy can give
relevant temperature values, even tc-grps are specified in mdp. Isn't?
> 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 restraints.
can you clarify how it can be practically done?
> 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?
yes, since non-reactive FF at high temperatures cannot be reliable due to
vibrational effects, all my MD has been done by reactive one.
> Your first post suggested the run was done with Gromacs (being that you
> had .tpr and .edr files).
I have produced .tpr file but not .edr.
> The outcomes you posted agree perfectly with constrained molecules,
The posted data refereed to un-reliability of g_traj for obtaining of T. I
just wanted to know the reason via comparison with g_energy. Those obtained
by non-reactive FF of OPLS.
> 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).
My molecules are not water and g_traj gave following T values for same
system using two different FFs
As i said already I just converted reaxff trajectory to gro one and also
used tpr file (constrain=none in mdp) for estimation of T with g_traj.
How constrained MD results (OPLS) can be corrected?
> 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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