[gmx-users] Test Particle Insertion of Water
s.neumann08 at gmail.com
Wed May 9 15:01:00 CEST 2012
thank you Javier, I will try both in this case.
On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo <jcb1 at um.es> wrote:
> 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.
> 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
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
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