On 7/10/14, 9:30 PM, Rasoul Nasiri wrote:
On Fri, Jul 11, 2014 at 12:58 AM, Justin Lemkul <jalem...@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?
No, you can't then. This also makes any sort of interpretation non-trivial; if
an atom dissociates from one group to which it was linked, the interpretation of
its new velocity when bonding to another group is now somewhat discontinuous, is
it not?
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?
You need to recalculate the number of degrees of freedom based on whatever
constraints there might be. You said there are none, so that may not be the
case. Please excuse the typo in the earlier message, "restraints" should be
"constraints."
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.
This is where I was getting confused. Your very first message said you had the
"same trajectory and input files" but clearly this is not true. You're
comparing apples and oranges; an accurate statement of what's really going on is
very important and saves everyone time.
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?
Now you're losing me again. You're talking about converting some ReaxFF
trajectory without constraints, but were there constraints in the OPLS
trajectory? Can you give an actual listing of commands and .mdp files (if
applicable) for what you're doing? This is all very confusing.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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