Hi, Mark, I use the command: grompp -f md.mdp -c eq2.gro -p conf.top -n md.ndx -o md.tpr -t eq2.trr and index file was makde from command make_ndx, I named the two methanes as methane1 and methane2. and my mdp file is :
integrator = sd ld_seed = -1 ; start time and timestep in ps tinit = 0 dt = 0.002 nsteps = 25000000 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 25000000 nstvout = 25000000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 500 ; every 1 ps nstenergy = 50000 ; every 100 ps ; Output frequency and precision for xtc file nstxtcout = 50 ; every 0.1 ps xtc-precision = 10000 xtc_grps = system ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz or none pbc = xyz ; nblist cut-off rlist = 1.0 domain-decomposition = no ; Turn off intermolecular interaction between CH4: energygrp_excl = Methane1 Methane2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw = 0.9 rvdw-switch = 0.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t = 1.0 ; Langevin friction constant (ps) ref_t = 300 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = No pcoupltype = isotropic tau_p = 5.0 compressibility = 4.5e-05 ref_p = 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ; OPTIONS FOR BONDS constraints = hbonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration unconstrained-start = yes ******************************************************* I can't understand why Methane1 is not an energy group. Thanks for your help. -Xianghong Qi On Wed, Nov 19, 2008 at 3:04 AM, Mark Abraham <[EMAIL PROTECTED]>wrote: > xianghong qi wrote: > >> Hi, Mark: >> I made the index file and call two methanes as methane1 and methane2 , >> then I set energygrp_excl = methane1 methane2, but when I run grompp, it >> said methane1 is not an energy group. What do you understand this problem? >> Thanks. -Xianghong Qi >> > > You haven't done what you think you've done. I can't tell what you've done > wrong because you haven't told me what you've done, i.e. examples and > command lines. My guess is that you didn't supply your index file to grompp, > so it can't tell what the definition is. > > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Some people make the world more special just by being in it.
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
