Dear expert, I am simulating the protein-ligand system.
Mdp file parameter are Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) vdw-type = Cut-off rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation the command line and out-put is shown for box preparation are as follow editconf_mpi -f process.pdb -o princ.pdb -box 11.4 10.7 10.7 -princ -c new system size : 8.576 4.832 4.220 shift : 5.003 5.426 6.257 (nm) new center : 5.700 5.350 5.350 (nm) new box vectors : 11.400 10.700 10.700 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume :1305.19 (nm^3) I put the 40 ns production run. When I checked the pbc by command g_mindist_mpi -od pbc-1.xvg -w -pi -s md.tpr -f md.xtc -b 12000 I got the following result.. The shortest periodic distance is 0.154938 (nm) at time 16162 (ps), between atoms 223 and 3270 Atom 223 is protein chain A atom and 3270 is chain B ( ligand atom) . I process on xtc file by -pbc nojump and got the nojump.xtc file I run the above g_mindist_mpi command on these XTC file . I get The shortest periodic distance is 3.39417 (nm) at time 12350 (ps), between atoms 2706 and 3241 So is my system is seeing its periodic image..and I have to rerun..??? (The box i used in simulation is larger than -d 1.0 ) Am I making mistake in comand line??? All suggestion are welcome . With best wishes and regards, Rama david. -- 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