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

[Jochen Hub]

csreddy at ncbs.res.in wrote:
> Dear Jochen,
> Sorry to bother you. I did not calculate the densities it is the program
> output!. Is this a bug?.
>   
Sorry to say that, but I don't have the feeling that it's my job to find 
the error in your calcuation...

> 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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-- 
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************