[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? mean square of this term gives us mean square displacment and the gromacs can do it by using g_msd is there any command that give us .(ri (t)-ri(0)) and not mean squre of it? -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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. The kinds of force fields ordinarily used for MD are unsuited for breaking and forming bonds. I strongly suggest searching the literature for relevant similar work, or being prepared for a lot of hard work. Or both. Mark -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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? mean square of this term gives us mean square displacment and the gromacs can do it by using g_msd is there any command that give us .(ri(t)-ri(0)) and not mean squre of it? -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 mdrun -deffnm md_0_1 But in between my computer got switched-off. My simulation is in half way (500ps). How i can concatenate the files to restart the simulation from 500ps. Thank you regards vidya -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 topol.top -n index.ndx -o md_0_1.tpr mdrun -deffnm md_0_1 But in between my computer got switched-off. My simulation is in half way (500ps). How i can concatenate the files to restart the simulation from 500ps. http://www.gromacs.org/Documentation/How-tos/Doing_Restarts -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
