[gmx-users] Re: Density Deferences between spc216 and tip4p

[Nagy, Peter I.]

In TIP4P there is a fourth center (called M) close to the O atom. It reveals from the output
that gromacs considers four atoms with this model but only three with SPC. If (this is a question)
a mass is assigned to M in TIP4P, the density calculated by the PROGRAM must be larger than
upon manual calculation and assuming 18 g for the molar mass of water
 
Peter Nagy

________________________________

From: gmx-users-bounces at gromacs.org on behalf of csreddy at ncbs.res.in
Sent: Thu 12/13/2007 5:04 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Re: Density Deferences between spc216 and tip4p



Dear Jochen,
Sorry to bother you. I did not calculate the densities it is the program
output!. Is this a bug?.

Regards
Chandu
> Message: 8
> Date: Thu, 13 Dec 2007 10:28:02 +0100
> From: Jochen Hub <jhub at gwdg.de>
> Subject: Re: [gmx-users] Density Deferences between spc216 and tip4p
>       water   models
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4760FB22.3030101 at gwdg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> csreddy at ncbs.res.in wrote:
>> Dear All,
>> I was trying  create a  box (cubic 10 10 10) of water. I am a bit
>> surprised by looking at the density deferences between spc216 and tip4p
>> water models. I am giving the brief output below.
>>
>> genbox -cs tip4p.gro -box 10 10 10
>>
>> Output configuration contains 131540 atoms in 32885 residues
>> Volume                 :        1000 (nm^3)
>> Density                :     1639.65 (g/l)
>> Number of SOL molecules:  32885
>>
> Theres is something wrong in your calculation of the density. From 32885
> Molcules (18g/mol) in a volume (10nm)^3 I get a density of 982 g/l.
>
> Cheers, Jochen
>>
>> genbox -cs spc2i6.gro -box 10 10 10
>>
>> Output configuration contains 99678 atoms in 33226 residues
>> Volume                 :        1000 (nm^3)
>> Density                :     993.966 (g/l)
>> Number of SOL molecules:  33226
>>
>> What would be the reason for this drastic differences in density? How
>> can
>> I make it into 1000 (g/l) by using above command.
>>
>> Thanks in advance.
>> Regards
>> Chandu
>>
>>
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>>
>
>
> --
> ************************************************
> Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> ************************************************
>
>
>
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