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?
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) 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 -- 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
