Thanks for your comments<br> I have a very crude question which may not be even logical to ask here but I just want to know your opinion on this:<br><br>If I will perform two simulations in following two ways :<br><br><b>RUN:1</b><br>
<br>(1) Did NVT with POSRES on protein and <br> gen_vel=yes <br> gen_temp= 350<br><br>(2) Did NPT with POSRES on protein and<br> continuation=yes <br> gen_vel=no ;Without reading velocities from NVT<br><br>(3) Did MD with No POSRES (NPT) <br>
continuation=yes<br> gen_vel=no ; No velocities read from previous run<br><br><br><b><br>RUN:2<br><br></b>(1) Did NVT with POSRES on protein and <br>
gen_vel=yes <br>
gen_temp= 350<br>
<br>
(2) Did NPT with POSRES on protein and<br>
continuation=yes <br>
gen_vel=no ; Reading velocities from NVT run using -t option<br>
<br>
(3) Did MD with No POSRES (NPT) <br>
continuation=yes<br>
gen_vel=no ; Velocities read from previous run using -t option<br><br><br><br>What will be the expected flaws of the RUN:1 over RUN:2 and will the results got from the RUN:1 is unreliable ? If yes why ?<br><br><br><br>
<div class="gmail_quote">On Fri, Apr 6, 2012 at 20:26, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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">On 7/04/2012 12:37 AM, Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
bipin singh wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks for your comments.<br>
One more question.<br>
Does Gromacs saves velocities in pdb files, when we use gen_vel=yes option in mdp and save the output(-c) of mdrun as pdb file instead of gro file.<br>
<br>
</blockquote>
<br>
No. Velocities are only saved in the .trr and/or .cpt files. There is no place for velocities in .pdb files.<br>
</blockquote>
<br></div>
It's conceivable that there are velocities in a mdrun -c finalstructure.gro file, but these would have to be only at low precision, and thus often useless.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="HOEnZb"><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br><span style="color:rgb(51,51,255)">-----------------------</span><br style="color:rgb(51,51,255)"><i><span style="color:rgb(51,51,255)">Regards,</span></i><br style="color:rgb(51,51,255)">
<span style="color:rgb(51,51,255);font-family:garamond,serif">Bipin Singh</span><br><br>