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
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 _______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
[email protected] [email protected] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
