[gmx-users] How to generate xvg files

[Mark Abraham]

Jack Shultz wrote:
> 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

Probably. See manual section 7.3.8

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

-x is not a flag - it accepts a filename / filename prefix. Omitting it 
entirely will probably generate traj.xtc. Experiment and see.

Mark

> 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
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> 
> 
>