Dear All,
During a simulation of a protein with a ligand, I see the -NH3 of the lysine side chain near the ligand is getting squeezed for a very short time; N-H bonds are getting contracted and the angle are no longer within tetrahedral normal <HNH angles. I have used LINCS to keep all the covalent C-H, N-H and O-H bonds rigid. I have gone through a string [ http://lists.gromacs.org/pipermail/gmx-users/2010-November/056094.html] in the mailing list but found little helpful. For my case the simulation does not give me any warning. Please suggest me if there is any problem with my simulation protocol. The '.mdp' file is given as follows integrator = md tinit = 0 dt = 0.001 nsteps = 5000000 nstcomm = 1 comm_grps = system comm_mode =linear ; 7.3.8 Output Control nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 2000 nstenergy = 2000 nstxtcout = 2000 xtc_precision = 2000 xtc_grps = System energygrps = System ; 7.3.9 Neighbor Searching nstlist = 10 ns_type = grid pbc = xyz rlist = 1.4 ; 7.3.10 Electrostatics coulombtype = PME rcoulomb = 1.4 ; 7.3.11 VdW vdwtype = cut-off rvdw = 1.4 DispCorr = EnerPres ; 7.3.13 Ewald fourierspacing = 0.14 pme_order = 4 ewald_rtol = 1e-5 ; 7.3.14 Temperature Coupling tcoupl = nose-hoover tc_grps = system tau_t = 1.0 ref_t = 300 ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300 gen_seed = 113969 ; 7.3.18 Bonds constraints = h-bonds constraint_algorithm = LINCS continuation = yes lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 Thanks, Tarak -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
