[gmx-users] Slow Runs

[Denny Frost]

about 12000 atoms, 8 nodes, CentOS 5.3/Linux, infiniband.  Below is a copy
of my mdp file.

title               =  BMIM+PF6
cpp                 =  /lib/cpp
constraints         =  all_bonds
integrator          =  md
dt                  =  0.004   ; ps !
nsteps              =  20000000   ; total 4ns.
nstcomm             =  1
nstxout             =  50000
nstvout             =  50000
nstfout             =  0
nstlog              =  5000
nstenergy           =  5000
nstxtcout           =  25000
nstlist             =  10
ns_type             =  grid
pbc                 =  xyz
coulombtype         =  PME
vdwtype             =  Shift
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
fourierspacing      =  0.6
;pme_order           =  4
ewald_rtol          =  1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc_grps             =  BMI      PF6
tau_t               =  0.1  0.1
ref_t               =  300  300
nsttcouple          =  1
; Energy monitoring
energygrps          =  BMI      PF6
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
pcoupltype          =  isotropic
;pc-grps             =  BMI      PFF
tau_p               =  1.0
ref_p               =  1.0
compressibility     =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  100000


On Thu, Jan 27, 2011 at 4:12 PM, Dallas Warren <Dallas.Warren at monash.edu>wrote:

> You will need to provide more details on the system.  How many atoms, what
> sort of computer system is it being run on, how many nodes, copy of the mdp
> file etc.
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu
>
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> *From:* gmx-users-bounces at gromacs.org [mailto:
> gmx-users-bounces at gromacs.org] *On Behalf Of *Denny Frost
> *Sent:* Friday, 28 January 2011 9:34 AM
> *To:* Discussion list for GROMACS users
> *Subject:* [gmx-users] Slow Runs
>
>
>
> I am taking over a project for a graduate student who did MD using Gromacs
> 3.3.3.  I now run similar simulations with Gromacs 4.5.1 and find that they
> run only about 1/2 to 1/3 as fast as the previous runs done in Gromacs
> 3.3.3.  The runs have about the same number of atoms and both use opls force
> fields.  The mdp files is virtually the same (I copied them).  The only
> major difference is that my runs have difference species and thus have
> different (although smaller) itp files.  The runs are stable and give
> reasonable thermodynamic properties - they're just slow.  Has anyone had any
> experience with something like this?
>
> --
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