Chandu, 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.
Tsjerk On Dec 13, 2007 11:04 AM, <[EMAIL PROTECTED]> wrote: > 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 <[EMAIL PROTECTED]> > > Subject: Re: [gmx-users] Density Deferences between spc216 and tip4p > > water models > > To: Discussion list for GROMACS users <[email protected]> > > Message-ID: <[EMAIL PROTECTED]> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > [EMAIL PROTECTED] 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 > >> > >> > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> 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 [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > >> . > >> > >> > > > > > > -- > > ************************************************ > > Jochen Hub > > Max Planck Institute for Biophysical Chemistry > > Computational biomolecular dynamics group > > Am Fassberg 11 > > D-37077 Goettingen, Germany > > Email: jhub[at]gwdg.de > > ************************************************ > > > > > > > > ------------------------------ > > > > _______________________________________________ > > gmx-users mailing list > > [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > > > End of gmx-users Digest, Vol 44, Issue 37 > > ***************************************** > > > > > > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
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