Thank you so much Mark. You are right about the cut-off values. I am now using 1.2nm which appears more commonly in literature. If possible please take a look at these statistics:
R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-Cycles Seconds % ----------------------------------------------------------------------- Neighbor search 1 380527 166719.792 59692.7 2.3 Force 1 3805262 1068307.182 382498.9 14.8 Write traj. 1 10433 1319.463 472.4 0.0 Update 1 3805262 12043.902 4312.2 0.2 Constraints 1 3805262 18769.536 6720.3 0.3 Rest 1 5965690.942 2135968.4 82.5 ----------------------------------------------------------------------- Total 1 7232850.817 2589664.9 100.0 ----------------------------------------------------------------------- NODE (s) Real (s) (%) Time: 2476509.010 2589664.940 95.6 28d15h55:09 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 16.281 468.817 0.266 90.391 Finished mdrun on node 0 Thu Oct 13 21:43:03 2011 It seems like "Rest" option is taking 82% time. Now would this correspond to an external program like plumed or is it something else? Regards Pooja On Mon, Oct 24, 2011 at 8:18 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 25/10/2011 9:54 AM, Sai Pooja wrote: >> >> Hi all, >> >> I am using GROMACS with the plugin PLUMED in double precision. The >> speed has gone down by a huge margin and I was wondering if there is >> something in 1) compilation 2) md parameters that could be >> contributing to this? > > Simply moving to double precision will slow things down noticeably. How much > depends on a lot of things, but you can test this yourself with a non-PLUMED > double-precision GROMACS. > > Otherwise, you should consider whether whatever you are doing with PLUMED is > expected to take a lot longer than normal... > >> >> md parameters: >> >> >> title = NVT simulation (constant number, volume and >> temperature) >> cpp = /lib/cpp >> define = -DPOSRES >> >> ; RUN CONTROL PARAMETERS >> integrator = md >> dt = 0.002 >> nsteps = 5000000 >> >> ; OUTPUT CONTROL OPTIONS >> nstxout = 0 ; ast frame (coordinates) >> nstvout = 2000 ; (velocities) >> nstfout = 2000 ; No output, except for last frame >> (forces) >> nstlog = 1000 ; Write every step to the log >> nstenergy = 1000 ; Write energies at every step >> xtc_grps = Protein Non-Protein >> nstxtcout = 500 ; Do not write a compressed trajectory >> energygrps = Protein SOL ; Write energy information >> separately for these groups >> ;energygrp_table = Protein SOL SOL SOL >> >> ; NEIGHBORSEARCHING PARAMETERS >> nstlist = 10 >> ns-type = Grid >> pbc = xyz >> rlist = 1.8 >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW >> coulombtype = Cut-off >> fourierspacing = 0.15 >> rcoulomb = 1.8 >> ;rcoulomb_switch = 1.6 >> epsilon_rf = 78 >> vdw-type = Cut-off >> rvdw = 1.8 >> ;rvdw-switch = 1.6 >> ;table-extension = 1.0 >> >> ; FFT grid size, when a value is 0 fourierspacing will be used = >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> ; EWALD/PME/PPPM parameters = >> pme_order = 4 >> ewald_rtol = 1e-05 >> epsilon_surface = 0 >> optimize_fft = no >> ; Temperature coupling >> tcoupl = nose-hoover >> tc-grps = Protein Non-Protein >> tau_t = 0.4 0.4 >> ref_t = 300 300 >> >> ; Pressure coupling >> pcoupl = no >> >> ; OPTIONS FOR BONDS >> constraints = all-bonds >> >> >> Details of the simulation: >> 1) MD with explicit solvent using charmm27 with tip3p (recommended one) > > Those cut-offs do not look like any I've ever seen for CHARMM force fields. > It is not wise to haphazardly choose large values for poor electrostatic > algorithms and hope for the best - even though almost all force fields were > parameterized with poor electrostatic treatments. > > Mark > >> 2) gromacs 4.5.1 >> 3) With plumed >> 4) Double precision >> 5) Position restraints for some parts of the protein (5 chains) >> >> >> I would really appreciate any help. >> >> >> Regards >> Pooja >> >> >> >> Pooja >> > > -- > 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 > -- Quaerendo Invenietis-Seek and you shall discover. -- 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