Justin, Again much obliged for your comments. They are most illustrative...
I would like to make a final note on the issue of these many e-mails... I am sure that GROMACS is fast, but that fast?...For the sake of knowing that we are doing the right things, this is our topol.top file in which we eliminated all POSRES for the Protein and DMPC, not so for the WATER...
------------- ; Include forcefield parameters #include "./gromos53a6_lipid.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Protein_chain_B.itp" #include "topol_Protein_chain_C.itp" ; Include water topology #include "./gromos53a6_lipid.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "./gromos53a6_lipid.ff/ions.itp" [ system ] ; Name mod.pdb [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 Protein_chain_C 1 ---------------------- On Protein_chain_A there are 342 atoms On Protein_chain_B there are 289 atoms On Protein_chain_C there are 715 atoms On DMPC there are 123 molecules of 46 atoms each On SOL there are 3205 molecules of 3 atoms each For a total of 16619 atomsI know that this is a medium size system for which I was expecting longer CPU time for a 20 ns MD run.
I know that there was no "error", which I meant is that I was surprised by the outcome...
May be GROMACS is as fast as it is claimed... Cheers, Ramon El 04/04/2011 05:27 p.m., Justin A. Lemkul escribió:
Dr. Ramón Garduño-Juárez wrote:Justin,Thank you for your comments after finishing the MD production run for up to 20 ns...Since this step was over very quickly, now I have a simple question ¿How long, in human time, should a production run last?There is no way to answer that. It depends on the hardware, number of atoms, system load, application of any number of the Gromacs algorithms, .mdp settings...The production run was carried out in six processors Intel Xeon (R) E5405 2.00 GHz. The last few lines of the md_0_1.log are:----------------------------------------- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 180685.417 180685.417 100.0 2d02h11:25 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 232.900 12.351 9.564 2.510 ----------------------------------------- Is this correct? In my opinion it should lasted much more longer...Nope, Gromacs is just fast :)Before reaching this point, this is an update of what we did...First we eliminated the SOL_SOL group and the only special index group was Protein_DMPC.Since the NVT equilibration failed, we took option # 2 of the "Advanced Troubleshooting", for the 1st phase of Equilibration.After this step we proceeded with the equilibration phase 2 with a 1-ns NPT equilibration which ended fine.Next, we proceeded with a 20 ns production run. Thus, the modified lines of the .mpd file found in the tutorial page were:nsteps = 10000000 ; 2 * 10000000 = 2000 ps (20 ns) tc-grps = Protein DMPC SOL comm-grps = Protein_DMPC SOL With this instructions the 20 ns simulation took 2d02h11:25 I believe the "error" comes from the line constrains = all-bonds which surely must be changed to constrains = none or hbondsWhy do you say that? What error is occurring? You said your simulations were running fine. You most certainly should not remove constraints if you're sticking with a 2-fs timestep. The system will be unstable without constraints. You might be able to get away with hbonds, but certainly not "none."-JustinLooking forward to your comments... Much obliged, Ramon
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