Denny Frost wrote:
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
This fourierspacing is 5-6 times larger than what is normally accepted as
sufficiently accurate. A sparse grid will make the PME algorithm faster,
actually, but at the expense of accuracy.
Can you post the domain decomposition statistics from the .log file? They
appear just above the energies from time 0. What did grompp tell you about the
relative PME:PP load?
-Justin
;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.war...@monash.edu
<mailto:dallas.war...@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.war...@monash.edu <mailto:dallas.war...@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-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>
[mailto:gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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