[gmx-users] compute displacement

I have performed a MD simulation with gromacs 4.0.7 the system that I have simulated contain 1000 atomes and now in order to compute intermediate scattering function F(q,t)=1/N<∑_(i=1)^N〖exp⁡(-iq.(r_i (t)-r_(i(0))> I need to compute (ri (t)-ri(0)) for all atomes and all times. how can I do this? me

Re: [gmx-users] Graphene growth simulation in gromacs

On 24/07/11, neclaoz wrote: > Hello gromacs users, > > I am trying to do a MD simulation of graphene growth using Gromacs. However I > don't know where to begin? Which potential should I use? So far I was only > involved in CNT simulations in gromacs, and I am confused about this growth.

[gmx-users] compute displacement

I have performed a MD simulation with gromacs 4.0.7 the system that I have simulated contain 1000 atomes and now in order to compute intermediate scattering function F(q,t)=1/N<∑_(i=1)^N〖exp⁡(-iq.(r_i (t)-r_(i(0))> I need to compute (ri (t)-ri(0)) for all atomes and all times. how can I do this? me

[gmx-users] concatenate md files

Dear Friends, I am doing simulation of a system containing a protein (T4 lysozyme L99A/M102Q) in complex with a ligand with the help of Justin tutorials. I ran following commands to perform production run (1000ps) grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_1.tpr md

Re: [gmx-users] concatenate md files

R.Vidya Rajendran (10PHD013) wrote: Dear Friends, I am doing simulation of a system containing a protein (T4 lysozyme L99A/M102Q) in complex with a ligand with the help of Justin tutorials. I ran following commands to perform production run (1000ps) grompp -f md.mdp -c npt.gro -t npt.cpt -p