[gmx-users] density_SW_model

[Sang-Min Park]

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    gmx-users at gromacs.org
>> 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 gmx-users-request at gromacs.org.
>> 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
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>