Hey Eli: What is the correlation observed between you and Moeed?
I suppose you eventually compressed your system so much, that it became very distorted. Check your GRO file. I believe it is not healthy inside. Regards. Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 On Thu, Jun 2, 2011 at 6:53 PM, Moeed <lecie...@googlemail.com> wrote: > Dear Dr.Chaban, > > I am so sorry to send you this message. Thank you for your comments. I have > encountered a problem that no one on the list could help much. I am very > hopeful you can assist me especially because I have noticed you respond to > messages dealing with compression or NPT runs. I am really confused since I > have been using the same input files (gro. top and mdp) and have been > collecting without any problem. Since yesterday I am getting a weird message > that is printed continuously until I kill mdrun. > > > arning: Only triclinic boxes with the first vector parallel to the x-axis > and the second vector in the xy-plane are supported. > Box (3x3): > Box[ 0]={ nan, nan, nan} > Box[ 1]={ nan, nan, nan} > Box[ 2]={ nan, nan, nan} > > I have only polyethylene chains in my system. I really appreciate if you > could help me or could kindly take a very brief look at my system. I can > send you top and gro files. I assure you top file is generated properly. I > have done many runs using that. Please let me know if you are interested. > > I thank you so much > > Waiting for your reply. > > Best regards, > Eli. > > > ; Run control > integrator = md > dt = 0.002 > nsteps = 1000000 ;5000 > nstcomm = 100 > > ; Output control > nstenergy = 100 > nstxout = 100 > nstvout = 0 > nstfout = 0 > nstlog = 1000 > nstxtcout = 1000 > > ; Neighbor searching > nstlist = 10 > ns_type = grid > > ; Electrostatics/VdW > coulombtype = Shift > vdw-type = Shift > rcoulomb-switch = 0 > rvdw-switch = 0.9 ;0 > > ; Cut-offs > rlist = 1.25 > rcoulomb = 1.0 ;1.1 > rvdw = 1.0 > > ; Temperature coupling > Tcoupl = v-rescale > tc-grps = System ;HEX > tau_t = 0.1 ;0.1 > ref_t = 300 ;300 > > ; Pressure coupling > Pcoupl = Parrinello-Rahman > Pcoupltype = isotropic > tau_p = 1 ;0.5 > compressibility = 4.5e-5 4.5e-5 > ref_p = 10 30 > > ; Velocity generation > gen_vel = yes > gen_temp = 300.0 > gen_seed = 173529 > > ; Bonds > constraints = all-bonds > constraint-algorithm = lincs > > > > > > > On 1 June 2011 14:59, Vitaly Chaban <vvcha...@gmail.com> wrote: >> >> Either a tighter pressure coupling time... >> >> >> >> >> On Wed, Jun 1, 2011 at 2:57 PM, Vitaly Chaban <vvcha...@gmail.com> wrote: >> > Hmm... >> > >> > >> > 1. The background of the task is not quite clear for me. >> > >> > 2. Evidently, the fluctuations are higher than the difference for your >> > pressures. >> > >> > 3. Why not to use significantly larger systems and significantly >> > larger difference between pressures? >> > >> > >> > >> > -- >> > Dr. Vitaly V. Chaban, Department of Chemistry >> > University of Rochester, Rochester, New York 14627-0216 >> > >> > >> > >> > >> >> >> >> I am trying to study the effect of pressure on total potential of my >> >> system >> >> (8 polymer chains). My problem is that I dont see a systematic effect >> >> of >> >> pressure on potentials and I cant judge if different pressures increase >> >> or >> >> decrease potential. This is the critical observable in my system and >> >> with >> >> high fluctuations I am getting I cant make comment on pressure effect. >> >> Total >> >> drift is high in most potential functions..I start my runs from a frame >> >> which is the output of an older NPT run (I use cpt file) that has a >> >> close >> >> density to what I want. In the production runs (NPT for 12 27 70 bar). >> >> >> >> Below is the settings I am using and I really appreciate it if you >> >> could >> >> comment on the most important factors for such a study. I tried >> >> different >> >> cutoffs as well...I though maybe increasing cutoffs invloves more >> >> interactions and can represent better the pressure effect... >> >> >> >> Thanks so much! >> >> >> >> >> >> ; Run control >> >> integrator = md >> >> dt = 0.002 >> >> nsteps = 1000000 ;5000 >> >> nstcomm = 100 >> >> >> >> ; Output control >> >> nstenergy = 100 >> >> nstxout = 100 >> >> nstvout = 0 >> >> nstfout = 0 >> >> nstlog = 1000 >> >> nstxtcout = 1000 >> >> >> >> ; Neighbor searching >> >> nstlist = 10 >> >> ns_type = grid >> >> >> >> ; Electrostatics/VdW >> >> coulombtype = Shift >> >> vdw-type = Shift >> >> rcoulomb-switch = 0.5 ;0 >> >> rvdw-switch = 0.9 ;0 >> >> >> >> ; Cut-offs >> >> rlist = 1.32 ;1.25 ; tired >> >> different >> >> cutoffs and r -switch... >> >> rcoulomb = 1.1 ;1.0 >> >> rvdw = 1.1 ;1.0 >> >> >> >> ; Temperature coupling >> >> Tcoupl = v-rescale >> >> tc-grps = System >> >> tau_t = 0.1 >> >> ref_t = 300 >> >> >> >> ; Pressure coupling >> >> Pcoupl = Parrinello-Rahman >> >> Pcoupltype = isotropic >> >> tau_p = 1 >> >> compressibility = 3.5e-5 >> >> ref_p = 10 >> >> >> >> ; Velocity generation >> >> gen_vel = no;yes >> >> gen_temp = 300.0 >> >> gen_seed = 173529 >> >> >> >> ; Bonds >> >> >> >> constraints = all-bonds >> >> constraint-algorithm = lincs >> >> >> >> >> >> results for 12 27 70 bar resp. >> >> >> >> >> >> Statistics over 2043101 steps [ 500.0000 through 4586.2000 ps ], 17 >> >> data >> >> sets >> >> >> >> All statistics are over 204311 points >> >> >> >> >> >> >> >> Energy Average Err.Est. RMSD Tot-Drift >> >> >> >> >> >> ------------------------------------------------------------------------------- >> >> >> >> LJ (SR) -634.358 2.9 11.0696 -20.3551 >> >> (kJ/mol) >> >> >> >> Coulomb (SR) 184.082 1.4 3.62712 9.04046 >> >> (kJ/mol) >> >> >> >> P*otential 642.528 6.4 23.1897 -44.6636 >> >> (kJ/mol)* >> >> >> >> Kinetic En. 904.294 0.075 16.2742 0.382223 >> >> (kJ/mol) >> >> >> >> Total Energy 1546.82 6.3 28.6865 -44.2813 >> >> (kJ/mol) >> >> >> >> Temperature 300.186 0.025 5.4023 0.126881 >> >> (K) >> >> >> >> Pressure 12.3856 0.89 887.501 5.41599 >> >> (bar) >> >> >> >> Density 824.417 2.1 9.27838 14.7965 >> >> (kg/m^3) >> >> >> >> >> >> >> >> >> >> >> >> Statistics over 750001 steps [ 500.0000 through 2000.0000 ps ], 17 data >> >> sets >> >> >> >> All statistics are over 75001 points >> >> >> >> >> >> >> >> Energy Average Err.Est. RMSD Tot-Drift >> >> >> >> >> >> ------------------------------------------------------------------------------- >> >> >> >> LJ (SR) -638.643 4.3 12.0718 -10.2094 >> >> (kJ/mol) >> >> >> >> Coulomb (SR) 184.51 1 2.89777 5.99117 >> >> (kJ/mol) >> >> >> >> *Potential 634.902 5.7 22.2857 -21.4761 >> >> (kJ/mol)* >> >> >> >> Kinetic En. 904.181 0.11 16.2261 -0.275076 >> >> (kJ/mol) >> >> >> >> Total Energy 1539.08 5.7 27.9661 -21.7511 >> >> (kJ/mol) >> >> >> >> Temperature 300.148 0.035 5.38636 -0.0913135 >> >> (K) >> >> >> >> Pressure 27.6467 1.4 881.409 8.58275 >> >> (bar) >> >> >> >> Density 826.734 3.4 9.76089 6.06824 >> >> (kg/m^3) >> >> >> >> >> >> >> >> >> >> >> >> 70 bar run >> >> >> >> >> >> even 6 ns runs gives large total drifts..e.g.13.4934 for density.. >> >> >> >> >> >> >> >> Statistics over 2750001 steps [ 500.0000 through 6000.0000 ps ], 17 >> >> data >> >> sets >> >> >> >> All statistics are over 275001 points >> >> >> >> >> >> >> >> Energy Average Err.Est. RMSD Tot-Drift >> >> >> >> >> >> ------------------------------------------------------------------------------- >> >> >> >> LJ (SR) -639.206 3.7 11.6741 -23.7773 >> >> (kJ/mol) >> >> >> >> Coulomb (SR) 182.97 1.7 4.18663 11.8694 >> >> (kJ/mol) >> >> >> >> *Potential 640.114 7.5 24.9191 -51.8187 >> >> (kJ/mol)* >> >> >> >> Kinetic En. 904.3 0.074 16.2887 0.161695 >> >> (kJ/mol) >> >> >> >> Total Energy 1544.41 7.5 30.1347 -51.657 >> >> (kJ/mol) >> >> >> >> Temperature 300.187 0.024 5.40713 0.0536754 >> >> (K) >> >> >> >> Pressure 69.7658 0.86 893.933 -2.29885 >> >> (bar) >> >> >> >> Density 829.657 2.3 8.98849 13.4934 >> >> (kg/m^3) >> > >> -- >> 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 > > -- 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