[gmx-users] Slow in double-precision version

[Mark Abraham]

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
>