[gmx-users] Post processing REMD simulation

[Mohammad Madani]

Dear Prof. Van der Spoel
Many thanks for your email.
In fact, I want to predict the structure of one highly disorder protein.  I
ran my Remd simulation for 16ns per each replica.  I Checked the trajectory
file of one of the replica randomly but I did not see any significant
change in comparison with my initial Structure.
I asked question about this issue from one of the professor in MIT, he
suggest me that because the structure is disordered it will be important to
characterize the ensemble you get out, rather than a single structure.

Now, I do not know what should I do with this.

Could you please help me with this?

Many thanks

On Sun, Apr 12, 2020 at 2:25 AM David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> *Message sent from a system outside of UConn.*
>
>
> Den 2020-04-12 kl. 05:40, skrev Mohammad Madani:
> > Dear all,
> > Hi.
> > I have problems about the analysis of the REMD simulation. I run the remd
> > for folding the protein.
> >
> > I have 191 replicas, the temperature range is 300K to 500K. I ran the
> > simulation 16 ns for each replica. and the exchange rate is between
> > 0.3-0.4.
> > Now, I have one trr file and one log file for each replica in its
> > temperature.
> > I do not how can analysis these outputs.
> >
> > Could you please help me with this?
>
> What would you like to analyze?
>
> You will have to write a couple of scripts to plot potential energy as a
> function of T for instance.
> >
> > Many thanks.
> >
> > Mohammad
> >
>
>
> --
> David van der Spoel, Ph.D.,
> Professor of Biology
> Uppsala University.
> http://virtualchemistry.org
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