[gmx-users] pullx and pullf

[shivangi nangia]

Is there any advantage(s) of doing a manual pull versus the pull code or
vice-versa?

Shivangi Nangia, Ph. D
Postdoctoral Research Associate
Department of Molecular and Cell Biology
University of Connecticut


On Fri, Jan 24, 2014 at 1:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/24/14, 1:21 PM, shivangi nangia wrote:
>
>> Is there a way around to generate similar data as in pullx/pullf.xvg
>> files (from
>> just md runs) without using the pull code.
>>
>>
> pullf.xvg contains pulling forces from the harmonic spring.  If you didn't
> apply any biasing potential, there is no force to report.  The pullx.xvg
> file simply reports the distance between the reference and pulled group;
> you can obtain the same information from g_dist.
>
> -Justin
>
>
>>
>>
>> Shivangi Nangia, Ph. D
>> Postdoctoral Research Associate
>> Department of Molecular and Cell Biology
>> University of Connecticut
>>
>>
>> On Fri, Jan 24, 2014 at 1:00 PM, Justin Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>>     On 1/24/14, 12:50 PM, shivangi nangia wrote:
>>
>>         Hello,
>>
>>         I am running a umbrella sampling but not using the pull code.
>>
>>         I have various starting configurations for a protein-bilayer
>> system.
>>         I am performing md runs for each configuration separately.
>>
>>         In order to use g_wham I need pullx/pullf .xvg files.
>>
>>         I have tried these commands:
>>
>>         1) mdrun_mpi -s nocard1.tpr -px ( to run the md simulation),
>> pullx.xvg is
>>         not generated
>>
>>         2) Post md run
>>
>>         mdrun_mpi -s nocard1.tpr -cpi nocard1_moved.cpt -rerun
>> nocard1_moved.xtc -px
>>
>>         pullx.xvg is still not generated.
>>
>>
>>     You will not get these output files unless you are using the pull
>> code.
>>
>>     -Justin
>>
>>     --
>>     ==============================__====================
>>
>>
>>     Justin A. Lemkul, Ph.D.
>>     Postdoctoral Fellow
>>
>>     Department of Pharmaceutical Sciences
>>     School of Pharmacy
>>     Health Sciences Facility II, Room 601
>>     University of Maryland, Baltimore
>>     20 Penn St.
>>     Baltimore, MD 21201
>>
>>     jalemkul at outerbanks.umaryland.__edu
>>     <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
>>     <tel:%28410%29%20706-7441>
>>
>>     ==============================__====================
>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
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