Sang-Min Park wrote:
Hello David,
thank you for your response.
Yes, this is the right mdp file.
The total system contains also a small NMA molecule (6 atoms), which
should not affect significantly the density (520 solvent molecules).
Sang Min
OK, I suggest that if you can reproduce the problem with only water
(easier for testing) that you submit a bugzilla.
I assume this is 4.0.x?
On Tue, 24 Feb 2009, David van der Spoel wrote:
Sang-Min Park wrote:
Dear all,
I ran a 1ns simulation in SW water (polarizable model) under NPT
(P=1 bar , T=300 K) conditions.
I checked the density and had a constant plateau value around 640 g/L
, which is obviously too low. I used the flexible and rigid version
(520 solvent molecules), with isotropic polarizability and used an
integrationstep of 0.5 fs (flexible) respectively 1 fs (rigid model).
The other parameters are taken as following : emtol = 0.1
emstep = 0.002
xtc_precision = 100000
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.4
vdwtype = cut-off
coulombtype = PME
fourierspacing = 0.12
pme_order = 4
optimize_fft = yes
tcoupl = Berendsen
tc-grps = Protein SOL
Do you have protein as well?
Otherwise, is this the correct mdp file?
tau_t = 0.1 0.1
ref_t = 300 300
Pcoupl = Berendsen
tau_p = 5
compressibility = 4.5e-5
ref_p = 1.0
What I have to change in order to reproduce the correct densities
(~1Kg/L) as reported in JPCB Vol 105 No.13 (2001) ? Thank you for
your time
Sang Min _______________________________________________
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________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
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David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
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
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
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