Chandu,<br><br>It's clear you didn't do the calculations. Please do them yourself and see what answer you get for the density of 32885 water molecules in a box with volume 10^3 nm^3. Note also that there may be implicit assumptions underlying the value of the density provided by genbox, but it's the number of molecules that counts.
<br><br>Tsjerk<br><br><div class="gmail_quote">On Dec 13, 2007 11:04 AM, <<a href="mailto:csreddy@ncbs.res.in">csreddy@ncbs.res.in</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Jochen,<br>Sorry to bother you. I did not calculate the densities it is the program<br>output!. Is this a bug?.<br><br>Regards<br>Chandu<br>> Message: 8<br>> Date: Thu, 13 Dec 2007 10:28:02 +0100<br>> From: Jochen Hub <
<a href="mailto:jhub@gwdg.de">jhub@gwdg.de</a>><br>> Subject: Re: [gmx-users] Density Deferences between spc216 and tip4p<br>> water models<br>> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a>><br>> Message-ID: <<a href="mailto:4760FB22.3030101@gwdg.de">4760FB22.3030101@gwdg.de</a>><br>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>><br>> <a href="mailto:csreddy@ncbs.res.in">
csreddy@ncbs.res.in</a> wrote:<br>>> Dear All,<br>>> I was trying create a box (cubic 10 10 10) of water. I am a bit<br>>> surprised by looking at the density deferences between spc216 and tip4p<br>>> water models. I am giving the brief output below.
<br>>><br>>> genbox -cs tip4p.gro -box 10 10 10<br>>><br>>> Output configuration contains 131540 atoms in 32885 residues<br>>> Volume : 1000 (nm^3)<br>>> Density :
1639.65 (g/l)<br>>> Number of SOL molecules: 32885<br>>><br>> Theres is something wrong in your calculation of the density. From 32885<br>> Molcules (18g/mol) in a volume (10nm)^3 I get a density of 982 g/l.
<br>><br>> Cheers, Jochen<br>>><br>>> genbox -cs spc2i6.gro -box 10 10 10<br>>><br>>> Output configuration contains 99678 atoms in 33226 residues<br>>> Volume : 1000 (nm^3)
<br>>> Density : 993.966 (g/l)<br>>> Number of SOL molecules: 33226<br>>><br>>> What would be the reason for this drastic differences in density? How<br>>> can<br>>> I make it into 1000 (g/l) by using above command.
<br>>><br>>> Thanks in advance.<br>>> Regards<br>>> Chandu<br>>><br>>><br>>> _______________________________________________<br>>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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>><br>>><br>><br>><br>> --<br>> ************************************************<br>> Jochen Hub<br>> Max Planck Institute for Biophysical Chemistry<br>> Computational biomolecular dynamics group
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<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931 <br>F: +31-30-2537623