[gmx-users] How to generate xvg files

[Jack Shultz]

I'm trying to get the xtc output. The mdp file has these parameters.
Is the nstxtcout what specifiies it to generate xtc?
nsteps          = 2000          ; Maximum number of (minimization)
steps to perform
nstenergy       = 10            ; Write energies to disk every nstenergy steps
nstxtcout       = 10            ; Write coordinates to disk every
nstxtcout steps

Do I need to use this -x flag?
mdrun -nice 0 -s em.tpr -x
No xtc was created though

On Tue, Nov 10, 2009 at 9:43 PM, Amit Choubey <kgp.amit at gmail.com> wrote:
>
>
> On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz <js at drugdiscoveryathome.com>
> wrote:
>>
>> Actually I guess I need to generate the xtc first before I can get the xvg
>>
>> I am trying to develop a workflow for this
>> mdrun
>> g dist calculates the distances between the centers of mass of two groups
>> g bond calculates distances between atoms
>> g msd calculates mean square displacements
>> g rms calculates rmsd’s with a reference structure and rmsd matrices
>> g rmsf calculates atomic fluctuations
>> g energy writes energies to xvg files and displays averages
>
> Thats true. First you need to do the simulation 'mdrun' and then analyze the
> trajectory (.xtc) and energy (.edr) files generated. It takes quite some
> time to figure out the first step 'mdrun' :)
> amit
>
>
>>
>> On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey <kgp.amit at gmail.com> wrote:
>> >
>> >
>> > On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz
>> > <js at drugdiscoveryathome.com>
>> > wrote:
>> >>
>> >> Hi I am trying to generate xvg files for my simulation. Which
>> >> parameter do I need to specify?
>> >
>> > xvg files for what? They are used for data files for 2D plots of
>> > quantities
>> > that can be analyzed...
>> > Can you be more specific?
>> > amit
>> >>
>> >> --
>> >> Jack
>> >>
>> >> http://drugdiscoveryathome.com
>> >> http://hydrogenathome.org
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>>
>>
>> --
>> Jack
>>
>> http://drugdiscoveryathome.com
>> http://hydrogenathome.org
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
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>
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-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org