[gmx-users] density_SW_model

[David van der Spoel]

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.
________________________________________________________________________
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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