[gmx-users] problem in umbrella sampling

[Justin Lemkul]

On 8/10/15 7:12 AM, Rajneet Kaur wrote:
> Hello sir,
> Thank you so much for response. I am beginner of gromacs. I  don't understand how to make summery_distance.dat and group. Text and  what is significance of these files in umbrella sampling

groups.txt is made in a text editor.  Its function is explained in the tutorial, 
but more generally:

http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

The summary_distances.dat file is the output of the Perl script that basically 
just acts as a wrapper of g_dist and summarizes the output.

-Justin

> Thanks and Regards,
> R.K
>
> Sent from my iPhone
>
>> On Aug 8, 2015, at 8:10 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>>> On 8/7/15 3:33 AM, Rajneet kaur Saini wrote:
>>> Dear Users,
>>> hi.. i am following justin umbrella sampling tutorial.i dont understand the procedure for umbrella sampling after this command:
>>> To extract the frames from your trajectory (traj.xtc), use trjconv (save the whole system, group 0, when prompted):trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep
>>> A series of coordinate files (conf0.gro, conf1.gro, etc) will be produced, corresponding to each of the frames saved in the continuous pulling simulation. To iteratively call g_dist on all of these (501!) frames that were generated, I have written a Perl script that takes care of this task. It will print a file called "summary_distances.dat" that contains this information. The script can be found here. We will need to make use of the index file again, as well as a text file called "groups.txt," which will be used to select our analysis groups non-interactively. The contents of groups.txt should be:19
>>> 20
>>> The groups.txt file can be created with a plain text editor. Once you have this file, change the .txt file extension of distances.txt (linked above) to .pl and execute the script:perl distances.pl
>>> Look at the contents of summary.dat to see the progression of COM distance between chain A and chain B over time. Make note of the configurations to be used for umbrella sampling, based on the desired spacing. That is, if you want 0.2-nm spacing, you might find the following lines in summary.dat:50     0.600
>>> ...
>>> 100    0.800
>>> You would then use conf50.gro and conf100.gro as the starting configurations of two adjacent umbrella sampling windows. Make note of all the configurations you wish to use before continuing. For the purposes of this tutorial, identifying configurations with 0.2-nm spacing will suffice, although in the original work a different (more detailed) spacing was used.I am using Gromacs 5.0.5
>>> Could anybody please explain me?????RegardsR.K
>>
>> What is it that you don't understand?
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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