<div>Thank you very much for your replay sir...<br></div><br><div class="gmail_quote">On Wed, Apr 14, 2010 at 5:36 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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 class="im"><br>
<br>
Bharath.K. Chakravarthi wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
sir should i set dat to 0 or what to do....<br>
<br>
</blockquote>
<br></div>
I clearly stated that you should set nstxtcout > 0 in my first message. Leaving any output control parameter set to zero means "produce output every zero steps" or essentially, not at all.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<br>
On Wed, Apr 14, 2010 at 5:32 AM, Bharath.K. Chakravarthi <<a href="mailto:bharath.chakravarthi@gmail.com" target="_blank">bharath.chakravarthi@gmail.com</a> <mailto:<a href="mailto:bharath.chakravarthi@gmail.com" target="_blank">bharath.chakravarthi@gmail.com</a>>> wrote:<br>
<br>
<br>
<br>
On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi<br>
<<a href="mailto:bharath.chakravarthi@gmail.com" target="_blank">bharath.chakravarthi@gmail.com</a><br></div><div class="im">
<mailto:<a href="mailto:bharath.chakravarthi@gmail.com" target="_blank">bharath.chakravarthi@gmail.com</a>>> wrote:<br>
<br>
Thank you for your kind replay sir....<br>
sir in my .mdp file there is nstxtout instead of nstxtcout sir<br>
and it is set to 500<br>
is this what u told...<br>
i have also attached the .mdp file in this mail sir<br>
<br>
On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul<br></div><div class="im">
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Bharath.K. Chakravarthi wrote:<br>
<br>
hi there i tried to run MD and i wanted to use *.xtc<br>
file in vmd to visualize the protein but unfortunately<br>
there is no such file i given the command like this<br>
mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x<br>
md_traj.xtc -c md_final.gro -e md_ener.edr<br>
as procedure this should create md_traj.xtc file rite.....<br>
<br>
<br>
Provided that you have set nstxtcout > 0 in the .mdp file.<br>
The default is 0 (no .xtc file). Consult the manual for<br>
appropriate settings.<br>
<br>
-Justin<br>
<br>
<br>
so please can u help me out of this mesh.......<br>
<br>
-- Bharath.K.Chakravarthi<br>
Ph:9535629260<br>
<br>
<br>
-- ========================================<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></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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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-- Bharath.K.Chakravarthi<br>
Ph:9535629260<br>
<br>
<br>
<br>
<br>
-- Bharath.K.Chakravarthi<br>
Ph:9535629260<br>
<br>
<br>
<br>
<br>
-- <br>
Bharath.K.Chakravarthi<br>
Ph:9535629260<br>
</div></blockquote><div><div class="h5">
<br>
-- <br>
========================================<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>
<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharath.K.Chakravarthi<br>Ph:9535629260<br>