Hello, I am trying a simulation for water dimer in vaccum (gas phase). Here I run the simulation with following steps
This is the .pdb file before energy minimization TITLE S C A M O R G REMARK THIS IS A SIMULATION BOX CRYST1 3.000 3.000 3.000 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 OW WAT 1 0.317 1.494 1.565 1.00 0.00 ATOM 2 HW1 WAT 1 -0.091 2.293 1.258 1.00 0.00 ATOM 3 HW2 WAT 1 -0.144 0.788 1.129 1.00 0.00 ATOM 4 OW WAT 2 3.172 1.515 1.356 1.00 0.00 ATOM 5 HW1 WAT 2 2.224 1.482 1.459 1.00 0.00 ATOM 6 HW2 WAT 2 3.522 1.427 2.231 1.00 0.00 TER ENDMDL I run the energy minimization grompp -f minim-gas.mdp -c dimer.pdb -p dimer.top -o dimer.tpr mdrun -pd -s dimer.tpr -o dimer.trr -c dimer.pdb -e dimer.edr -g dimer.log I got the following file which I could visualize TITLE Protein MODEL 1 ATOM 1 OW WAT 1 0.351 1.490 1.592 1.00 0.00 ATOM 2 HW1 WAT 1 -0.106 2.335 1.248 1.00 0.00 ATOM 3 HW2 WAT 1 -0.162 0.750 1.112 1.00 0.00 ATOM 4 OW WAT 2 3.198 1.519 1.321 1.00 0.00 ATOM 5 HW1 WAT 2 2.174 1.481 1.457 1.00 0.00 ATOM 6 HW2 WAT 2 3.544 1.423 2.268 1.00 0.00 TER ENDMDL minim-gas.mdp file title = cpeptide cpp = /usr/bin/cpp constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 50000 nstlist = 1 coulombtype = cut-off vdwtype = cut-off ns_type = simple rlist = 0.0 rcoulomb = 0.0 rvdw = 0.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes pbc = no ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 the I run equlibration grompp -f minim-pr.mdp -c dimer.pdb -p dimer.top -o dimer.tpr mdrun -pd -s dimer.tpr -o dimer.trr -c dimer.pdb -e dimer.edr -g dimer.log I got the following file which I could not visualize TITLE Protein MODEL 1 ATOM 1 OW WAT 1 -2737.208 974.242-2091.510 1.00 0.00 ATOM 2 HW1 WAT 1 -2737.949 973.910-2090.885 1.00 0.00 ATOM 3 HW2 WAT 1 -2736.363 974.004-2091.048 1.00 0.00 ATOM 4 OW WAT 2 2740.655-971.0932094.500 1.00 0.00 ATOM 5 HW1 WAT 2 2740.852-971.7332093.873 1.00 0.00 ATOM 6 HW2 WAT 2 2740.420-971.4722095.431 1.00 0.00 TER ENDMDL the equlibration file I used title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.001 ; ps ! nsteps = 1000000 ; total 1.0 ps. nstcomm = 1 nstxout = 10000 nstvout = 10000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = simple comm_mode = none coulombtype = cut-off vdwtype = cut-off rlist = 0.0 rcoulomb = 0.0 rvdw = 0.0 pbc = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = nose-hoover tau_t = 0.1 tc-grps =system ref_t = 298 ; Pressure coupling is on Pcoupl = NO ;Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 298.0 gen_seed = 173529 Is ther any thing wrong with my mdp files. WHy they is so much change is cooridnates in the .pdb file. I am using gromacs version 4.0.7. Thanks Nilesh -- 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
