<br><br><div class="gmail_quote">On Tue, Nov 10, 2009 at 7:02 PM, Jack Shultz <span dir="ltr"><<a href="mailto:js@drugdiscoveryathome.com">js@drugdiscoveryathome.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
I'm trying to get the xtc output. The mdp file has these parameters.<br>
Is the nstxtcout what specifiies it to generate xtc?<br></blockquote><div>yes its the freq of writing co - ordinates </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
nsteps = 2000 ; Maximum number of (minimization)<br>
steps to perform<br>
nstenergy = 10 ; Write energies to disk every nstenergy steps<br>
nstxtcout = 10 ; Write coordinates to disk every<br>
nstxtcout steps<br>
<br>
Do I need to use this -x flag?<br>
mdrun -nice 0 -s em.tpr -x<br>
No xtc was created though<br></blockquote><div>-x is for writing xtc file</div><div><a href="http://manual.gromacs.org/current/online/mdrun.html">http://manual.gromacs.org/current/online/mdrun.html</a> should help</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5"><br>
On Tue, Nov 10, 2009 at 9:43 PM, Amit Choubey <<a href="mailto:kgp.amit@gmail.com">kgp.amit@gmail.com</a>> wrote:<br>
><br>
><br>
> On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz <<a href="mailto:js@drugdiscoveryathome.com">js@drugdiscoveryathome.com</a>><br>
> wrote:<br>
>><br>
>> Actually I guess I need to generate the xtc first before I can get the xvg<br>
>><br>
>> I am trying to develop a workflow for this<br>
>> mdrun<br>
>> g dist calculates the distances between the centers of mass of two groups<br>
>> g bond calculates distances between atoms<br>
>> g msd calculates mean square displacements<br>
>> g rms calculates rmsd’s with a reference structure and rmsd matrices<br>
>> g rmsf calculates atomic fluctuations<br>
>> g energy writes energies to xvg files and displays averages<br>
><br>
> Thats true. First you need to do the simulation 'mdrun' and then analyze the<br>
> trajectory (.xtc) and energy (.edr) files generated. It takes quite some<br>
> time to figure out the first step 'mdrun' :)<br>
> amit<br>
><br>
><br>
>><br>
>> On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey <<a href="mailto:kgp.amit@gmail.com">kgp.amit@gmail.com</a>> wrote:<br>
>> ><br>
>> ><br>
>> > On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz<br>
>> > <<a href="mailto:js@drugdiscoveryathome.com">js@drugdiscoveryathome.com</a>><br>
>> > wrote:<br>
>> >><br>
>> >> Hi I am trying to generate xvg files for my simulation. Which<br>
>> >> parameter do I need to specify?<br>
>> ><br>
>> > xvg files for what? They are used for data files for 2D plots of<br>
>> > quantities<br>
>> > that can be analyzed...<br>
>> > Can you be more specific?<br>
>> > amit<br>
>> >><br>
>> >> --<br>
>> >> Jack<br>
>> >><br>
>> >> <a href="http://drugdiscoveryathome.com" target="_blank">http://drugdiscoveryathome.com</a><br>
>> >> <a href="http://hydrogenathome.org" target="_blank">http://hydrogenathome.org</a><br>
>> >> --<br>
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>><br>
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>><br>
>> --<br>
>> Jack<br>
>><br>
>> <a href="http://drugdiscoveryathome.com" target="_blank">http://drugdiscoveryathome.com</a><br>
>> <a href="http://hydrogenathome.org" target="_blank">http://hydrogenathome.org</a><br>
>> --<br>
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><br>
><br>
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><br>
<br>
<br>
<br>
--<br>
Jack<br>
<br>
<a href="http://drugdiscoveryathome.com" target="_blank">http://drugdiscoveryathome.com</a><br>
<a href="http://hydrogenathome.org" target="_blank">http://hydrogenathome.org</a><br>
--<br>
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</div></div></blockquote></div><br>