<HTML dir=ltr><HEAD><TITLE>[gmx-users] Re: Density Deferences between spc216 and tip4p</TITLE>
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<DIV dir=ltr><FONT face=Arial color=#000000 size=2>In TIP4P there is a fourth center (called M) close to the O atom. It reveals from the output</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2>that gromacs considers four atoms with this model but only three with SPC. If (this is a question)</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2>a mass is assigned to M in TIP4P, the density calculated by the PROGRAM must be larger than</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2>upon manual calculation and assuming 18 g for the molar mass of water</FONT></DIV>
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<DIV dir=ltr><FONT face=Arial size=2>Peter Nagy</FONT></DIV></DIV>
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<FONT face=Tahoma size=2><B>From:</B> gmx-users-bounces@gromacs.org on behalf of csreddy@ncbs.res.in<BR><B>Sent:</B> Thu 12/13/2007 5:04 AM<BR><B>To:</B> gmx-users@gromacs.org<BR><B>Subject:</B> [gmx-users] Re: Density Deferences between spc216 and tip4p<BR></FONT><BR></DIV>
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<P><FONT size=2>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 <jhub@gwdg.de><BR>> Subject: Re: [gmx-users] Density Deferences between spc216 and tip4p<BR>> water models<BR>> To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>> Message-ID: <4760FB22.3030101@gwdg.de><BR>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<BR>><BR>> csreddy@ncbs.res.in 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 gmx-users@gromacs.org<BR>>> <A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>>> Please search the archive at <A href="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before<BR>>> posting!<BR>>> Please don't post (un)subscribe requests to the list. Use the<BR>>> www interface or send it to gmx-users-request@gromacs.org.<BR>>> Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR>>><BR>>> .<BR>>><BR>>><BR>><BR>><BR>> --<BR>> ************************************************<BR>> Jochen Hub<BR>> Max Planck Institute for Biophysical Chemistry<BR>> Computational biomolecular dynamics group<BR>> Am Fassberg 11<BR>> D-37077 Goettingen, Germany<BR>> Email: jhub[at]gwdg.de<BR>> ************************************************<BR>><BR>><BR>><BR>> ------------------------------<BR>><BR>> _______________________________________________<BR>> gmx-users mailing list<BR>> gmx-users@gromacs.org<BR>> <A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>> Please search the archive at <A href="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!<BR>><BR>> End of gmx-users Digest, Vol 44, Issue 37<BR>> *****************************************<BR>><BR><BR><BR><BR><BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the<BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR></FONT></P></DIV></BODY></HTML>