[gmx-users] Slow in double-precision version

[Sai Pooja]

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.Abraham at 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
>>
>
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