[gmx-users] high pressure and temperatures: force field parameters

Thu Sep 8 21:47:11 CEST 2016

My apologies, I had intended for my response to be addressed to Mohsen, not Sotririos. 

-Micholas

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Smith, Micholas D. <smithmd at ornl.gov>
Sent: Thursday, September 08, 2016 3:44 PM
To: Discussion list for GROMACS users
Subject: [UNTRUSTED] Re: [gmx-users] high pressure and temperatures: force      field   parameters

Hi Sotririos,

I am not sure if anyone has ever done a detailed study of the extremes for each force-field; however, I can say from personal experience that what would be considered high (relative to physiological) temperature (~450K) simulations seem to perform relatively well for systems of with organic liquids in them. For instance binary systems that exhibit closed miscibility gaps can (such as Tetrahydrofuran-Water systems) experimentally, can have these same gaps/phase separation behaviors observed in MD simulations (even with TIP3P) with common force-fields (given a large enough simulation box).

I am inclined to believe that so long as you near not too close to a phase transition for your system, the standard force-fields will be at least reasonable approximations; that being said, this is more of an opinion gleened from experience simulating biopolymers at moderately high temps, than from any rigorous test. To be honest, it would be an interesting paper if someone did test the temperature and pressure bounds of force-field validity for protein behaviour.

When in doubt, you can always try to hunt down an experimentalist who may be able to inform you of some type of macroscopic/mesoscopic behavior that only occurs near the temperature/pressure you are interested for a similar system and see if you can get simulation results that are consistent with this before running your protein of interest under those cases.

Interesting question though...I'll have to take a longer literature search to see what that brings up.

===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
Sent: Thursday, September 08, 2016 3:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] high pressure and temperatures: force field    parameters

Hi Sotirios,

I totally agree with what you said. However, I am not interested in
breaking bonds or forming bonds (e.g. in plasma case)

To clarify the question, here is an example:

How if you want to check the effect of high temperature on protein
structure (folding and unfolding problem)? Or if you want to do a simulated
annealing! How much are you allowed to raise the temperature?!
(for now, lets assume unfolding and folding can happen in allowed time
scales. Lets focus on ff validity for a moment)

Is the ff developed for proteins are valid in high temperatures? We know
they are working well in physiological range. However, there are some cases
of interest where high T happens.

Hope it is clear now. The same for pressure.

Cheers
Mohsen

On Thu, Sep 8, 2016 at 10:42 AM, Sotirios Dionysios I. Papadatos <
si.papadatos at edu.cut.ac.cy> wrote:

> I am not aware on your question per se, but just to give you food for
> thought. Force fields are not based on real values of let's say force
> constants. You can't produce for example 'plasma' at least with the default
> ff, if you overheat. So it not a matter of a ff not being accurate for high
> values of T or P, rather than a ff is made to reproduce - simulate the
> physical properties of a system as close as possible to real life
> conditions. Now, if you are interested in simulating on such high values,
> you should search if there is a literature on how to simulate in such
> environments specifically.
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mohsen
> Ramezanpour <ramezanpour.mohsen at gmail.com>
> Sent: Thursday, September 8, 2016 2:47:07 AM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] high pressure and temperatures: force field parameters
>
> Dear gromacs users,
>
> Force field parameters are not usually parametrized for high pressures and
> temperatures.
>
> say for P=500 bar! or for T=500 K
>
> Although we can do simulations, but we cannot trust on the results.
>
> Is there any maximum (or range ) defined somewhere in the literature (which
> I am not aware of) we should not go further in simulations?
> I searched but I did not get any good answer for it.
>
> The best way would be to check the force field validity by comparing the
> simulations (with that FF) in desired high T and P with some available
> experimental data, even if these systems are not the same with what you are
> interested in. If they are valid, so, we might do predictions for our
> system of interest in those T and P range. Well, this also can be argued,
> because, the force field might not work properly for our specific molecules
> in question.
>
> Please let me know your opinion
>
> Thanks in advance
>
> Cheers
> Mohsen
>
>
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