Hello, I have run 2 ns simulations on a hydrocarbon system (initial density of ~ 2 SI and box size is 15 nm), one with version 4.0.7 and the other trial using 4.5.3. Both runs are almost equilibrated to 70 bar pressure but one is giving density of above 600SI (4.0.7) and the other density of around 15 SI (4.5.3). With 4.5.3 applying 100 bar pressure does not comrades the system either to the desired density. I need to study the system at different pressures from 1 to 70 bar, and I am wondering if the system can not be compressed with these ref_p values how can I keep the pressure fixed at P < 70 bar!?
Please help if you have any idea on why these two versions are giving inconsistent results and which one is reliable. Thanks so much, 4.0.7 Statistics over 250001 steps [* 1500.0001 thru 2000.0001 ps ],* 14 data sets The term 'Cons. rmsd ()' is averaged over 2501 frames All other averages are exact over 250001 steps Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Angle 36.9945 0.806738 0.804483 0.0521993 0.208798 Ryckaert-Bell. 9.04227 0.376253 0.371412 0.0521057 0.208424 LJ-14 5.23048 0.119612 0.119611 0.00033983 0.00135933 Coulomb-14 -1.66329 0.104171 0.102175 0.0175753 0.0703015 LJ (SR) -27.3967 0 0 0.0421934 0.168774 Coulomb (SR) 8.98711 0.163579 0.16062 -0.0268199 -0.10728 Potential 31.1944 0 0 0.137594 0.550377 Kinetic En. 51.1009 0.987759 0.987724 0.00725949 0.0290381 Total Energy 82.2953 0 0 0.144851 0.579408 Temperature 299.98 5.79849 5.79828 0.000340897 0.170449 *Pressure (bar) 69.3587 414.279 414.256 0.0298385 14.9193* Cons. rmsd () 4.01744e-06 1.41883e-07 1.41883e-07 0 0 *Box-X 3.04882 0 0 3.57512e-06 0.00178757 Box-Y 3.04882 0 0 3.57512e-* ----------------------------- 4.5.3. [* 1500.0001 thru 2000.0001 ps ],* Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Angle 37.1357 0.071 0.812307 -0.099711 (kJ/mol) Ryckaert-Bell. 9.17677 0.14 0.445934 -0.529281 (kJ/mol) LJ-14 5.18878 0.0087 0.137673 -0.03119 (kJ/mol) Coulomb-14 -1.60372 0.051 0.126405 -0.144403 (kJ/mol) LJ (SR) -4.24478 0.29 0.742141 0.697187 (kJ/mol) Coulomb (SR) 8.97451 0.082 0.198278 0.232025 (kJ/mol) Potential 54.6272 0.31 1.20733 0.124627 (kJ/mol) Kinetic En. 51.1047 0.021 0.9945 -0.066306 (kJ/mol) Total Energy 105.732 0.31 1.58869 0.058321 (kJ/mol) Temperature 300.002 0.12 5.83806 -0.389239 (K) *Pressure 66.734 5.3 91.83 11.5294 (bar) * Constr. rmsd 2.2661e-10 2.3e-10 3.58302e-08 -1.3595e-09 () *Box-X 11.0055 0.082 0.175309 -0.496198 (nm) Box-Y 11.0055 0.082 0.175309 -0.496198 (nm)* pbc = xyz integrator = md dt = 0.002 nsteps = 1000000 nstcomm = 100 nstenergy = 100 nstxout = 100 nstlist = 10 ns_type = grid coulombtype = Shift vdw-type = Shift rcoulomb-switch = 0 rvdw-switch = 0.9 rlist = 1.2 rcoulomb = 1.2 rvdw = 1.0 Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 300 Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1 compressibility = 4.5e-5 4.5e-5 ref_p = 70 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 constraints = all-bonds constraint-algorithm = lincs
-- 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
