thank you Javier, I will try both in this case. On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo <[email protected]> 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. > > Javier > > 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 > > > > -- > Javier CEREZO BASTIDA > PhD Student > Physical Chemistry > Universidad de Murcia > Murcia (Spain) > Tel: (+34)868887434 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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