thank you Javier, I will try both in this case.<br><br><div class="gmail_quote">On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo <span dir="ltr"><<a href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Steven<br>
<br>
As I remember, TPI is based on the calculation of the potential at
every conformation from the already computed simulation (inserting
the particle in every snapshot), so velocities are not used.<br>
<br>
Anyway, use both and see if there are any differences.<br>
<br>
Javier<br>
<br>
El 09/05/12 11:27, Steven Neumann escribió:
<div><div class="h5"><blockquote type="cite">Dear Gmx Users,<br>
<br>
I am running TPI of the water in the system containing free amino
acids. Steps:<br>
<br>
1. I run the NPT simulation of 100 ns to equilibrate the system.<br>
2. I added 1 extra water molecule to the final pdb file (converted
from gro) and to topology<br>
3. I creaded tpi.tpr using grompp using new pdb file with extra
water molecule<br>
4. mdrun –s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi
tpi298.xvg -tpid tpid298.xvg<br>
<br>
My question: Is it better generate new velocities in my mdp file
(continuation = yes, gen_vel = no, tpi integrator) for a pdb file
or use velocities from previous simulations (gro file)? <br>
If the second option is more appropriate what velocity shall I
adjust to the extra water molecule?<br>
<br>
I will appreciate your reply.<br>
<br>
Steven<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div><span class="HOEnZb"><font color="#888888"><div>-- <br>
Javier CEREZO BASTIDA<br>
PhD Student<br>
Physical Chemistry<br>
Universidad de Murcia<br>
Murcia (Spain)<br>
Tel: <a href="tel:%28%2B34%29868887434" value="+34868887434" target="_blank">(+34)868887434</a>
</div>
</font></span></div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br>