Thanks a lot Justin for the very helpful answers concerning the pressure equilibration. Using Berendsen Barostat over 200 ps has lead to the correct average pressure... I have another issue to discuss with you and with the Gromacs mailing list members; I have been trying to run a simulation on a computer cluster for the first time using a sub file script. What happened is that the .sub file attempted to run the simulation 24 times instead of parallelizing it over the 24 processors!!!! Here are the contents of run_1.sub file I tried to use to parallelize the simulation using qsub run_1.sub #PBS -S /bin/bash #PBS -N run_1 #PBS -l nodes=3:ppn=8 module load openmpi/gnu mpirun -np 24 /home/hassan/bin/bin/mdrun_mpi -deffnm run_1 -v &> run_1_update.txt exit $?
What happens it that it outputs 24 run_1.log files, starting from #run_1.log1# all the way to #run_1.log23#...Has anyone faced this problem before? and If yes, any hints or solutions? I do appreciate any help in that domain Hassan ________________________________ From: [email protected] on behalf of Justin A. Lemkul Sent: Mon 12/6/2010 6:43 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] pressure fluctuations Hassan Shallal wrote: > Dear Gromacs users, > > I have some concerns about the both the pressure fluctuations and > averages I obtained during the equilibration phase. I have already read > through several similar posts as well as the following link > http://www.gromacs.org/Documentation/Terminology/Pressure. I understand > the pressure is a macroscopic rather than instantaneous property and the > average is what really matters. I also found out through similar posts > that negative average pressure indicates the system tendency to contract. > > In the above link, it mentioned that pressure fluctuations should > decrease significantly with increasing the system's size. In my cases, I > have a fairly big systems (case_1 with *17393* water molecules > and case_2 with *11946 *water molecules). However, the pressure still > has huge fluctuations (around 500 bars) from the reference value (1 > bar). Here are the average pressure and density values resulting from > the equilibration phases of two cases, please notice the negative > average pressure values in both cases... > > Case_1_pressure: > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > Pressure *-2.48342* 0.92 369.709 -4.89668 > (bar) > Case_1_density: > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > Density 1022.89 0.38 3.8253 2.36724 > (kg/m^3) > Case_2_pressure: > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > Pressure *-8.25259* 2.6 423.681 -12.1722 > (bar) > Case_2_density: > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > Density 1034.11 0.37 2.49964 1.35551 > (kg/m^3) > > So I have some questions to address my concerns: > 1- each of the above systems has a protein molecule, NaCl to give 0.15 M > system and solvent (water) molecules... Could that tendency to contract > be an artifact of buffering the system with sodium and chloride ions? > I suppose anything is possible, but given that these are fairly standard conditions for most simulations, I tend to doubt it. My own (similar) systems do not show this problem. > 2- how to deal with the tendency of my system to contract? Should > I change the number of water molecules in the system? > or > Is it possible to improve the average pressure of the above systems by > increasing the time of equilibration from 100 ps to may be 500 ps or > even 1 ns? > > 3- Is there a widely used range of average pressure (for ref_p = 1 bar) > that indicates acceptable equilibration of the system prior to the > production? > To answer #2 and #3 simultaneously - equilibration is considered "finished" when your system stabilizes at the appropriate conditions (usually temperature and pressure). Your results indicate that your equilibrium is insufficient. > 4- I can't understand how the system has a tendency to contract whereas > the average density of the solvent is already slightly higher than it > should be (1000 kg/m^3). The contraction causes the density to rise. Pressure and density are not independent; density is a result of pressure. > I would like to ignore the pressure based judgement of the above > equilibration given that the average density values are very close to > the natural value (1000 kg/m^3) (by the way I am using tip3p water model > with CHARMM27 ff) Any comment!! > It is not guaranteed that simulation water models will reproduce the real (experimental) density of water. If memory serves, the expected density of TIP3P should be ~0.98 g mL^{-1}, but I could be wrong. > 5- Is the huge fluctuation of the pressure values of the above system > despite thier large sizes still acceptable? or large fluctuation is only > acceptable for small size systems and is unacceptable for large size > systems? > If it is unacceptable, any idea of how could it be alleviated or minimized? > The fluctuations seem reasonable. You might try equilibrating with the Berendsen barostat first, then switching to Parrinello-Rahman. The P-R barostat allows for wider fluctuations, so if the system is poorly equilibrated, your system will be slower to converge. -Justin > I am including the .mdp used in the above equilibration in case it is > needed. > > Any feedback or response to the above questions is so much appreciated.. > > Great regards > Hassan > > .mdp used for the above equilibration > define = -DPOSRES ; position restrain the protein > ; Run parameters > integrator = md ; leap-frog integrator > nsteps = 25000 ; 4 * 25000 = 100 ps > dt = 0.004 ; 4 fs, virtual sites along with heavy hydrogens are used > ; Output control > nstxout = 100 ; save coordinates every 0.2 ps > nstvout = 100 ; save velocities every 0.2 ps > nstenergy = 100 ; save energies every 0.2 ps > nstlog = 100 ; update log file every 0.2 ps > ; Bond parameters > continuation = yes ; Restarting after NVT > constraint_algorithm = lincs ; holonomic constraints > constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 6 ; also related to accuracy, changed to 6 because of > using virtual sites along with a larger time step > ; Neighborsearching > ns_type = grid ; search neighboring grid cells > nstlist = 5 ; 20 fs > rlist = 1.2 ; short-range neighborlist cutoff, equal to rcoulomb to > allow for PME electrostatics (in nm) > ; Lennard-Jones > vdwtype = switch ; VDW interactions are switched of > between 1 and 1.2 > rvdw_switch = 1 ; > rvdw = 1.2 ; short-range vdw cutoff, optimal for > CHARMM27 ff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics > pme_order = 4 ; cubic interpolation > rcoulomb = 1.2 ; short-range electrostatic cutoff, optimal for CHARMM27 > ff (in nm) > ; Temperature coupling is on > tcoupl = V-rescale ; modified Berendsen thermostat > tc-grps = Protein Non-Protein ; two coupling groups - more accurate > tau_t = 0.1 0.1 ; time constant, in ps > ref_t = 300 300 ; reference temperature, one for each group, in K > ; Pressure coupling is on > pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT > pcoupltype = isotropic ; uniform scaling of box vectors > tau_p = 1 ; in ps > ref_p = 1.0 ; reference pressure, in bar > compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > DispCorr = EnerPres ; account for switch vdW scheme > ; Velocity generation > gen_vel = no ; Velocity generation is off > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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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