[gmx-users] pullx and pullf

[Justin Lemkul]

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

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