[gmx-users] Test Particle Insertion of Water

Javier Cerezo jcb1 at um.es
Wed May 9 14:45:29 CEST 2012

Hi Steven

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.

Anyway, use both and see if there are any differences.


El 09/05/12 11:27, Steven Neumann escribió:
> 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

PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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