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

[Sotirios Dionysios I. Papadatos]

Now the part about sim annealing clarifies things a bit (if again I got it right of course). I recently read a study about simulations on cyclic peptides. They raised the temp up to 1000 K (maybe even more). The reason is that in cases such are these, you use extreme values to "jump over" energy barriers. Now the output is certainly not correct, but keep in mind that you are interested for a system of lower temp. Now for higher temps than a physiological range, the default ff, won't provide good results.

Topics such as this, that have a good educational debate should be posted as a wiki after they are "closed", for future reference.

________________________________
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 10:27:43 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
>
>
> --
> *Rewards work better than punishment ...*
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



--
*Rewards work better than punishment ...*
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.