Hello sir, Thanks for your reply. I have used this .mdp file. Is there anything wrong in the mdp file which I am using ? To tell you in detail : First I have done energy minimization. Output of this step (box_em.pdb) is used to create an index group for sol and cl- ions using make_ndx. Then I am trying to run grompp using this particular .mdp file before position restraint mdrun.
*pr.mdp file :* title = protein in popc bilayer cpp = /usr/bin/cpp define = -DPOSRES -DPOSRES_LIPID constraints = all-bonds constraint-algorithm= Lincs integrator = md dt = 0.002 nsteps = 5000 nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 vdw-type = Cut-off rvdw = 1 ; Berendsen temperature coupling is on in two groups tcoupl = berendsen tc_grps = Protein POPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps = Protein POPC SOL_CL- ; Pressure coupling is on Pcoupl = berendsen tau_p = 2.0 2.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 Pcoupl_type = semiisotropic ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Thanking you, Pawan On Thu, Apr 9, 2009 at 10:38 AM, Mark Abraham <[email protected]>wrote: > Pawan Kumar wrote: > >> Hello Mark Sir, >> >> I have tried that way also. >> The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p >> topol.top -o box_pr.tpr >> But this time i get an error like this "Atom 1 defined in multiple groups >> (1 & 3). " >> How to overcome this error ? >> > > You can't have the same atom in multiple groups used for the same purpose > within mdrun (e.g. T-coupling or energy). I guess you've constructed your > index file in a manner that is inconsistent with your use of it. > > > 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 >
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