Hi justin , Thank you for reply. Mdp parameters are as follow , ; 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)
I choose the protein for g_mindist option.. Please could you explain me what am getting and why it is not violation of pbc???? Sorry for these basic question, but I am confuse with these result With best wishes and regards, Rama david. On Sat, Nov 10, 2012 at 6:55 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/10/12 5:42 AM, rama david wrote: > >> 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 >> >> > You shouldn't use -b here. You should be checking the entire trajectory > for problems. > > > 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) . >> >> > What group did you choose for analysis, System? This is not a problem. > PBC artifacts only arise when a molecule sees itself. > > > 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 >> >> > This also looks fine, given the cutoffs described above, even without > knowing what these atoms are. > > > >> >> >> >> So is my system is seeing its periodic image..and I have to rerun..??? >> >> > I see no evidence of a problem. > > > (The box i used in simulation is larger than -d 1.0 ) >> >> Am I making mistake in comand line??? >> >> > Aside from what's noted above, no. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
