Shutting off the fft optimization produced the same results for
3.2.1. Then I tried running two simulations using version 3.3.1 with
the optimized fft and they differed. Your response seemed to imply
that the newer version should produce identical results. Could you
clear this up for me?
Thank you,
Jim Fonseca
On May 16, 2007, at 9:40 AM, Jim Fonseca wrote:
Thanks a lot--that was it.
On May 15, 2007, at 12:42 PM, David van der Spoel wrote:
Jim Fonseca wrote:
Hi,
Does anyone know what would cause a simulation to change if I run
it a second time? I'm starting with an EM structure and just
doing a quick 10 ps simulation. I've found that (in one case)
the energies start to differ somewhere between step 200 and step
250--the Vir and Pres values differ first. I can't figure out
what else besides gen_vel and gen_seed would give me different
results. I'm running on the same system, same number of
processors, etc. I'm pasting my .mdp below. I realize I'm
probably overlooking something, but can anyone help me with this?
Thank you,
Jim Fonseca
title = PG_Ca_ext
cpp = /usr/bin/cpp
include = -I../top
constraints = all-bonds
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 10000 ;20 ps
nstxout = 10000
nstvout = 10000
nstlog = 10000
nstenergy = 50
nstxtcout = 50
xtc_grps = Protein SOL_Na_Ca POP
energygrps = Protein SOL_Na_Ca POP
nstlist = 10
ns_type = grid
rlist = 1.4
coulombtype = PME
rcoulomb = 1.4
rvdw = 1.4
tcoupl = Berendsen
tc-grps = Protein SOL_Na_Ca POP
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
Pcoupl = Berendsen
pcoupltype = anisotropic
tau_p = 1.0
compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
ref_p = 1.5 1.5 1.5 0.0 0.0 0.0
gen_vel = yes
gen_temp = 300
gen_seed = 161803
optimize_fft = yes
Is this 3.2.1? The optimize_fft may make your simulations differ
because, depending on timing, a different algorithm may be used.
Change this flag to no and test again.
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--
David.
_____________________________________________________________________
___
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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