On 14 April 2011 02:11, Mark Abraham <[email protected]> wrote:
> On 14/04/2011 3:40 PM, Moeed wrote: > > > > On 13 April 2011 18:45, Mark Abraham <[email protected]> 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? > > > What does a set of charges with positive potential energy want to do? > > > Can you please elaborate on compressing using simulated annealing? How > can I do this? > > > That's not what I said - I used quotation marks and the word "style" for a > reason. I told you not to do massive changes of conditions, and to use small > increments of delta-P. Equilibrate at one P, change it a bit. Repeat. This > is like simulated annealing, but with P instead of T. > Dear Mark, I see now what you mean. But actually my problem is not equilibrating..I can follow your advise and equilibrate the system but as I said starting from the same structure and settings, both runs one with 4.0.7 and the other 4.5.3, show that system is pretty close to ref_p = 70 but densities are terrible different. What I dont realize is that how to judge which version is giving correct density. and also version 4.5.3 does not compress with any pressure below 100 bar. So even when I compress using 4.0.7, and try to use output structure from 4.0.7 as input for 4.5.3 to apply say ref_p of 70, my box expands again. I am stuck on this and it seems the only option is to just stick to version 4.0.7! :) > > Mark > > > 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 [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 >> > > > > -- > 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 >
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