Hi Dr. Spoel, Thanks for your reply! I set my script as follows:
gmx pdb2gmx -f water.pdb -o water.gro -water tip3p << EOF #water.pdb is a pdb file contains a single water molecule 5 #OPLS 2 #TIP3P EOF gmx editconf -f water.gro -o water_newbox.gro -c -d 1.5 -bt cubic gmx solvate -cp water_newbox.gro -cs spc216.gro -o water_solv.gro -p topol.top gmx grompp -f em.mdp -c water_solv.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr gmx mdrun -deffnm nvt gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr gmx mdrun -deffnm npt gmx grompp -f md1.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr #a short 200 ps run gmx mdrun -deffnm md_0_1 gmx grompp -f md2.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_2.tpr #a longer 2 ns run gmx mdrun -deffnm md_0_2 gmx trjconv -s md_0_2.tpr -f md_0_2.trr -o md_0_2_noPBC.trr -pbc mol -ur compact << EOF 2 #SOL (water) EOF gmx hbond -f md_0_2_noPBC.trr -s md_0_2.tpr -num hbnum.xvg -temp 298.15 -ac hbac.xvg << EOF 2 #SOL (water) 2 #SOL (water) EOF Here is the specification of my md*.mdp file ; Run parameter integrator = md ; leap-frog integrator dt = 0.002 ; ps ! nsteps = 1000000 ; total 2 ns ; Output control nstxout = 50 ; save coordinates every 100 fs nstvout = 0 nstenergy = 50 ; save energy every 100 fs nstlog = 50 ; Bond parameters continuation = yes constraint_algorithm = SHAKE shake-tol = 0.0001 constraints = all-bonds ; Neighborsearching cutoff-scheme = Verlet ns_type = grid nstlist = 5 rcoulomb = 1.0 rvdw = 1.0 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Temperature coupling is on Tcoupl = berendsen tc-grps = SOL tau_t = 0.1 ref_t = 298.15 ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic compressibility = 4.5e-5 tau_p = 1.0 ref_p = 1.0 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; Dispersion correction DispCorr = EnerPres gen_vel = no Could you take a look at my parameters and script and let me know if there is anything that might cause the deviation? Thanks!! Ben -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.