Hi D_Roy, The warning message is quite self-explanatory. Do read beyond the word WARNING. As for the other question, the constraint algorithm stands apart from the forcefield, unlike many other options. You can safely use Lincs with G536.
Cheers, Tsjerk On Mar 17, 2012 10:31 AM, "D_Roy" <r.dipan...@gmail.com> wrote: I trying to do an NVT simulation of a peptide in water with the following mdp parameters: ==== title = GROMOS53A6 NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstxtcout = 100 ; save coordinates to trajectory every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run ;bond constraint constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained constraint_algorithm = SHAKE ; shake_tol = 0.0001 ; relative tolerance ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.8 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics and ven der Waals coulombtype = Reaction-Field ; reaction-field for long-range electrostatics vdw-type = Cut-off ; van der Waals treatment for long-range electrostatics epsilon_rf = 62 ; dielectric constant/relative permitivitty ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ========== When I run grompp with the command: grompp -v -f pr.mdp -c protein_mod1_EM_solv.gro -p protein_mod1.top -o protein_mod1_PR.tpr I get a warning which reads: WARNING 1 [file 1DU9_mod1.top, line 1651]: With twin-range cut-off's and SHAKE the virial and the pressure are incorrect. However, when I delete the constraint_algorithm and shake_tol prameters from the mdp file allowing grompp to use the defualt LINCS algorithm, grompp doesn't complaint. Can any one help me as to why grompp complains when SHAKE is used but not with LINCS? The forcefield paper used SHAKE as constraint algorithm. Should I stay with SHAKE or use LINCS instead? By the way I am using GROMOS53A6 force field for the simulation. Thanks all. ----- Research Assistant Sikkim Manipal University DE -- View this message in context: http://gromacs.5086.n6.nabble.com/grompp-warning-with-SHAKE-but-ok-with-LINCS-tp4627513p4627513.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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