On Dec 8, 2010, at 1:03 PM, Hassan Shallal wrote: > 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? This typically happens when using a serial mdrun. You should check with ldd whether mdrun_mpi is linked to the correct mpi library.
Carsten > > I do appreciate any help in that domain > Hassan > > From: gmx-users-boun...@gromacs.org 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 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 > > -- > 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. 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