[gmx-users] mdrun

[MUSYOKA THOMMAS]

Dear Dr Justin,
Much appreciation. You nailed it.
Kind regards.


On Tue, Nov 5, 2013 at 2:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote:
>
>> Dear Users,
>> I am running MD simulations of a protein-ligand system. Sometimes when i
>> do
>> an mdrun, be it for the energy minimization or during the nvt and npt
>> equillibration  or the actual md run step, sometimes the output files are
>> named in a very odd way (strange extensions) e.g em.gro.tprr or
>> md.tpr.cpt,
>> md.tpr.xtc.
>>
>> Can anyone explain the cause of this?
>>
>>
> You are issuing the command in a way that you probably don't want.  I
> suspect what you are doing is:
>
> mdrun -deffnm md.tpr
>
> The -deffnm option is for the base file name and should not include an
> extension.  mdrun is only doing what you tell it; you're saying, "all my
> files are named md.tpr, and you can put whatever the necessary extension is
> on them."
>
> What you want is:
>
> mdrun -deffnm md
>
> -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 | (410) 706-7441
>
> ==================================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 

*MUSYOKA THOMMAS MUTEMIMob nos **+27844846540*
*B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science
(Nagasaki University)*

*PhD Student-Bioinformatics (Rhodes University)*Skype ID- MUSYOKA THOMMAS
MUTEMI
Alternative email - thommas at sia.co.ke








*"Do all the good you can, By all the means you can, In all the ways you
can, In all the places you can,At all the times you can,To all the people
you can,As long as ever you can." - John Wesley. *