[gmx-users] Replica exchange MD analysis

[Justin Lemkul]

On 3/25/19 2:22 PM, Rituraj Purohit wrote:
> Thank you Mark for the reply. In my REMD results I would like to
> observe the structure transition with temperature given variation (I
> think it is most common observation). My query here is the output of
> REMD, It does not give .xtc file but only .edr, .log and .gro
> even-thou I indicated -x .xtc during job submission. Is it possible to
> perform analysis with .edr, .log & .gro files and without the
> Trajectory file? If yes, Please let me know how to do different
> analysis such as RMSD, RMSF, Rg etc..

All of those depend on coordinates over time, i.e. the trajectory. Your 
existing files cannot be used for such analysis. You will only get an 
.xtc file if you specify a non-zero value of nstxout-compressed in the 
.mdp file.

-Justin

> regards
> RajP
>
> On Mon, Mar 25, 2019 at 6:43 PM Mark Abraham <mark.j.abraham at gmail.com> wrote:
>> Hi,
>>
>> This is the same as for any other scientific experiment. You need to have
>> thought about what you hope to learn and what you need to record in order
>> to analyse the results. REMD is essentially no different here.
>>
>> Mark
>>
>> On Sun., 24 Mar. 2019, 10:51 Rituraj Purohit, <riturajpurohit94 at gmail.com>
>> wrote:
>>
>>> Dear Friends,
>>> I performed REMD by following tutorial provided by Mark Abraham, But I
>>> am not able to get the analysis part. Is a step-wise tutorial
>>> available ? I would be thankful to you if anyone of you could help me
>>> to perform analysis of REMD output. Thanking you
>>> Regards
>>> RajP
>>> --
>>> 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.

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================