[gmx-users] Test Particle Insertion of Water

Steven Neumann s.neumann08 at gmail.com
Wed May 9 11:27:56 CEST 2012

Dear Gmx Users,

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

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
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.

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