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
>>
>
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