>From your system information, I understand that you need to specify tabulated potentials between atoms P and P, and between atoms C and P, and so on.
To achieve this, you need to create energy groups with atom types P and C, and specify energygrp_table options in the grompp such as following .... energygrps = P C ; (and rest of the groups in your system, you will need to specify index file containing energy groups ) energygrp_table = P P P C .... so now mdrun looks for table_P_P.xvg and table_P_C.xvg in the run directory, and uses it for P-P and P-C interactions, whereas for all other interactions default table.xvg file is used. I hope this helps. Regards Sikandar On Tue, Nov 15, 2011 at 2:49 PM, Liu, Liang <liu4...@gmail.com> wrote: > I am trying to use a serial of tabulated potentials, which are the > functions of the distance between atoms and the names are table.xvg, > table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some > RNA structures. > The procedure I apply is as following: > > pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce > editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 > genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top > grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 > mdrun -v -s em.tpr -c em.pdb -table table.xvg > > And the em.mdp file is: > cpp = /usr/bin/cpp ; Preprocessor > include = -I../top ; Directories to include in > the topology format > define = -DFLEX_SPC > integrator = steep ; Algorithm options > dt = 0.002 ; ps ! ; run control, the time step > nsteps = 1000 ; run steps, simulation > length = dt*nsteps > nstenergy = 10 ; Write energies to disk > every nstenergy steps > nstxtcout = 10 ; Write coordinates to disk > every nstxtcout steps > xtc_grps = RNA ; Which coordinate group(s) > to write to disk > energygrps = RNA ; Whici energy group(s) to > write to disk > nstlist = 10 ; Frequency to update the > neighbor list and long range forces > ns_type = grid ; Method to determine > neighbor list and long range forces (simple, grid) > rlist = 1.0 ; Cut-off for making > neighbor list (short range forces) > vdw-type = user > coulombtype = user ; Treatment of long range > electrostatic interactions > rcoulomb = 1.0 ; long range electrostatic > cut-off > rvdw = 1.0 ; long range Van der Walls > cut-off > constraints = none > pbc = xyz > emtol = 5000.0 > emstep = 0.01 > > All the procedure and file are right? Thanks. > > -- > Best, > Liang Liu > > -- > gmx-users mailing list gmx-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 mailing list gmx-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