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

[Rasoul Nasiri]

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:
>
>> 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,


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

1- ReaxFF
 0      399.321
 1      400.25
 2      401.08
 3      401.271
 4      400.67
 5      400.264
 6      400.752
 7      401.178
 8      401.391
 9      399.065
10      401.78

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.

2- OPLS
 0      269.581
 1      271.064
 2      271.309
 3      271.205
 4      271.499
 5      270.868
 6      272.247
 7      271.59
 8      271.614
 9      270.598
 10     271.662


How constrained MD results (OPLS) can be corrected?



Rasoul



> -Justin
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
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