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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:
<blockquote
cite="mid:CAKZJqQF__J3eLnSMdZLnBhttQRTX-dqzNbur_+xcnBeOmSUsGA@mail.gmail.com"
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>
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<br>
</blockquote>
<br>
<div class="moz-signature">-- <br>
Javier CEREZO BASTIDA<br>
PhD Student<br>
Physical Chemistry<br>
Universidad de Murcia<br>
Murcia (Spain)<br>
Tel: (+34)868887434
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