[gmx-users] Test Particle Insertion of Water
jcb1 at um.es
Wed May 9 14:45:29 CEST 2012
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
> 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.
Javier CEREZO BASTIDA
Universidad de Murcia
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users