On 15/04/2011 5:55 AM, Moeed wrote:
On 14 April 2011 02:11, Mark Abraham <[email protected] <mailto:[email protected]>> wrote:On 14/04/2011 3:40 PM, Moeed wrote:On 13 April 2011 18:45, Mark Abraham <[email protected] <mailto:[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..
Your problem *is* equilibrating. Clearly 4.5.3 is not doing it.
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.
Sure, so something got broken in at least one of these. I think you're being too rough.
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.
You're trying to draw deductions based on the doubtful premise that you can just apply a massive overpressure and the numerical integration will cope. Think about it - massive external pressure means lots of collisions and large velocities which mean large atomic motions over finite time steps. You've just left the integration step the same size, so I'm actually a bit surprised 4.0.7 appears to have coped. A gentler progressive compression will leave the system close to equilibrium throughout, and is much more likely to achieve a sensible result.
I am stuck on this and it seems the only option is to just stick to version 4.0.7!
I'm going to stop repeating myself soon :-) I think you're being too rough, and that 4.5.3 is getting unlucky and breaking and that 4.0.7 might be getting lucky.
Mark
:) MarkThanks, :) 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. Mark4.0.7 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 stepsEnergy 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 0.208424LJ-14 5.23048 0.119612 0.119611 0.00033983 0.00135933Coulomb-14 -1.66329 0.104171 0.102175 0.0175753 0.0703015 LJ (SR) -27.3967 0 0 0.0421934 0.168774Coulomb (SR) 8.98711 0.163579 0.16062 -0.0268199 -0.10728Potential 31.1944 0 0 0.137594 0.550377Kinetic En. 51.1009 0.987759 0.987724 0.00725949 0.0290381Total Energy 82.2953 0 0 0.144851 0.579408Temperature 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] <mailto:[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] <mailto:[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing list [email protected] <mailto:[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] <mailto:[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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