Re: [gmx-users] Number of atoms is very high

ok..thank you very much On 26 February 2013 23:54, Justin Lemkul wrote: > > > On 2/26/13 5:50 PM, Divya Sunil wrote: > >> Hello >> >> I have a protein consists of 2303 atoms. I simulated it in water using >> cubic box. As the protein has a long tail, the n

Re: [gmx-users] Number of atoms is very high

ring the total > number of atoms under 1 lakh. > > :) > > Cheers, > > Tsjerk > > > On Tue, Feb 26, 2013 at 11:50 PM, Divya Sunil > wrote: > > Hello > > > > I have a protein consists of 2303 atoms. I simulated it in water using > > cubic b

[gmx-users] MD with Xenon

hello, I have a protein in which I fixed Xenon in the binding sites. without xenon, I used GROMOS96 53a6 force field for simulation. With Xenon, which forcefield am I able to use? thanking you regards Divya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

Re: [gmx-users] Xe atom

thanks for the reply.. I am planning to place Xe in the protein binding site ( just like a metal atom). I made a topology file with xe charge and mass. I have two options to implement the simulation. 1. like protein-ligand simulation. 2. replacing a number of solvent (water) molecules with xe in th

Re: [gmx-users] Xe atom

> Dr. Vitaly V. Chaban > > > On Tue, Jul 9, 2013 at 10:39 AM, Divya Sunil >wrote: > > > thanks for the reply.. I am planning to place Xe in the protein binding > > site ( just like a metal atom). I made a topology file with xe charge and > > mass. I have two optio

Re: [gmx-users] Xe atom

non-bonded > section and you are ready to explore the binding. > > > > > Dr. Vitaly V. Chaban > > > On Wed, Jul 10, 2013 at 12:04 PM, Divya Sunil >wrote: > > > ya.. but there is experimental data to confirm the presence. can you help > > me to solve t