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

Fri Sep 9 01:15:32 CEST 2016

Hi Smith,

Thanks for your comment.

Interesting. However, not sure if in other cases, (different systems,
different molecules, T and P values) this will give good approximations.

In case, if ff are not valid, it might result in strange phase behaviours
and properties which are not even close to reality, which can be
misleading.

Regarding these, do you think we can predict anything and trust MD results
where there is no experimental data available?

To make it simple for now, lets assume that all system set-up, force field
and MD parameters are giving reasonable data compared to available
experimental data (either in physiological T and P range, or even for other
systems like yours in high T values). Can we generalize this idea and say
this ff might behave properly on my system (different molecules) in T
values of ~500 K, which is close to yours?!

Thanks in advance for your reply

Cheers
Mohsen

On Thu, Sep 8, 2016 at 1:47 PM, Smith, Micholas D. <smithmd at ornl.gov> wrote:

> 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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