sanni at theochem.uni-frankfurt.de
Tue Feb 24 22:08:09 CET 2009
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).
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.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
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