[gmx-users] Post processing REMD simulation

[David van der Spoel]

Den 2020-04-12 kl. 08:36, skrev 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?

When you say you don't see any changes, have you visually inspected all 
the final structures?

Another thing you can try is concatenate the trajectories from the 10 or 
20 lowest temperature and run clustering analysis.

Unfortunately 16 ns is not very long because it takes time to change 
conformation. It is also far from certain that your temperature exchange 
worked over the whole range, that is that structures cycled from 300K to 
500K and back.

The demux.pl script in the gromacs distribution may help analyzing that 
if it still works.
> 
> 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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-- 
David van der Spoel, Ph.D.,
Professor of Biology
Uppsala University.
http://virtualchemistry.org