<div>that means generating a trajectory file for every 10 steps rite <br></div><div>then i may need more disk space</div><div><br></div><div><br></div><br><div class="gmail_quote">On Tue, Apr 20, 2010 at 11:41 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="word-wrap:break-word"><br><div><div class="im"><div>On Apr 20, 2010, at 7:39 PM, Bharath.K. Chakravarthi wrote:</div>
<br><blockquote type="cite"><div>no i did not used -v flag at that command may be thats the mistake</div><div>thank u Justin</div><div><br></div><div class="gmail_quote">On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><br> <br> Bharath.K wrote:<br> <blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
I'm using gromacs-3.3.3 and here is the parameter<br> <br> ..<br> ..<br> nstxout = 500<br> nstvout = 1000<br> nstfout = 0<br> nstlist = 100<br></blockquote></div></blockquote>
</div></blockquote></div>This might not be the best choice! it is generally kept under 10! It depends on your</div><div>system/force field though....<div><div class="h5"><br><blockquote type="cite"><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
nstlog = 100<br> nstenergy = 10<br> nstxtcout = 500<br> ..<br> ..<br> <br> for writing trajectories in .mdp file and what is check point file and -cpi file.cpt ...<br> i did not get u.... :(<br>
<br> </blockquote> <br></div> This is why stating your Gromacs version at the outset is useful. Checkpointing was introduced in Gromacs 4.0, so you won't be able to use it.<br> <br> You also have not answered my first question. What is your mdrun command line? Did you use the -v flag? If not, you will not get any information about completion time. There is nothing that the .mdp options or tpbconv will do for you as far as completion time is concerned.<br>
<font color="#888888"> <br> -Justin</font><div><div><br> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole <<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>> wrote:<br>
<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <br>
>tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000<br> this shows last step before crashing and starts from there until 1000<br> <br> </blockquote> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
then<br> <br> >mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log -<br> e minim_ener_01.edr<br> <br> </blockquote> <br> Nothing seem particularly wrong! May be you write your trajectory file<br> too often! Did the original the indicated the same amount of data to be<br>
written?<br> <br> which version of gmx you are using? actually using the check point<br> file is relatively easy (-cpi fie.cpt to add to mdrun) and does all<br> the work for you!<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br> </blockquote> <br> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <br> On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole <<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>><br>
wrote:<br> <br> On Apr 20, 2010, at 9:14 AM, Bharath.K wrote:<br> <br> Hello all....<br> i got a system crash at some steps..<br> after creating the new .trr file using command tpbconv<br> trr file with tpbconv? you mean tpr?<br>
and running MDS<br> what is MDS?<br> <br> by mdrun command the approximate finishing time is not showing.....<br> and also a warning is showing as<br> <br> WARNING: this run may generate approximately 4583292 Mb of data....<br>
That is a bit enormous<br> <br> <br> is there any changes that i should do while giving the command and<br> can i continue with this warning.....<br> Which exact command did you use?<br> <br> <br> <br> -- <br> Bharath.K<br>
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</div><div> ========================================<br> <br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br> MILES-IGERT Trainee<br> Department of Biochemistry<br> Virginia Tech<br> Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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