[gmx-users] density_SW_model

[David van der Spoel]

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.
>> ________________________________________________________________________
>> 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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> _______________________________________________
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++