On 13 April 2011 18:45, Mark Abraham <mark.abra...@anu.edu.au> wrote:
> On 14/04/2011 10:22 AM, Moeed wrote: > > 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. > > > Why are your potential energies positive? What does the final configuration > look like? Why aren't you doing a "simulated annealing" style of compression > with small increments of delta-P? (These, coincidentally are even good data > for your study...) Massive leaps in ensemble conditions are often > poorly-conditioned for numerical integration. You're generating velocities > that are only approximately correct, not giving them any chance to > equilibrate, and then smashing the system with massive over-pressure. Small > wonder it might sometimes break... > Hi Mark, You mean I should get negative potential? I am sure topology is generated properly. can you explain why this is concerning? Can you please elaborate on compressing using simulated annealing? How can I do this? Thanks, :) > > When reporting output from .log file and g_energy, please either use plain > text email, or switch to a non-proportional font like Courier. Those tables > make it harder for people to help you than you want it to be. > > Mark > > > > 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 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 >
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