[gmx-users] Test Particle Insertion of Water

[Steven Neumann]

Dear Gmx Users,

I am running TPI of the water in the system containing free amino acids.
Steps:

1. I run the NPT simulation of 100 ns to equilibrate the system.
2. I added 1 extra water molecule to the final pdb file (converted from
gro) and to topology
3. I creaded tpi.tpr using grompp using new pdb file with extra water
molecule
4. mdrun –s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi tpi298.xvg
-tpid tpid298.xvg

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)?
If the second option is more appropriate what velocity shall I adjust to
the extra water molecule?

I will appreciate your reply.

Steven
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120509/2bfbfc57/attachment.html>