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Hi,<br><br>Force fields have usually been parametrized with one specific water model.<br>For all GROMOS force fields this water model is SPC.<br>The people behind GROMOS would recommend you not to use any other<br>water model.<br><br>I have tested thermodynamic properties of GROMOS with SPC and SPC/E<br>and I would say that SPC/E actually performs slightly better than SPC<br>(and SPC/E is a better model for water than SPC), see:<br>http://dx.doi.org/10.1021/jp0641029<br><br>For configuration (gro) file, it does not matter much which starting configuration<br>you use, since you anyhow have to (re)equilibrate the solvent after you<br>solvate your solute. The differences in conformation between all 3-site<br>water models are minimal and will dissappear after a few hundred steps.<br><br>Berk<br><br>> Date: Thu, 13 Nov 2008 20:47:46 +0530<br>> From: suman@sscu.iisc.ernet.in<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] GROMOS with SPC/E water?<br>> <br>> Dear all,<br>> <br>> I am a little confused with the statement in the pdb2gmx man page: "with<br>> GROMOS we recommend SPC, with OPLS, TIP4P: spc , spce ..."<br>> <br>> What is the specific reason behind this recommendation? What kind of<br>> problems there might be if I want to use SPC/E water for a polymer<br>> (hydrocarbon) in water system within ffG43a2 force field?<br>> <br>> <br>> Second part of my question:<br>> <br>> The Gromacs topology directory provides only spc216.gro file. Is the<br>> configuration file (to be used with genbox) same for both spc and spce?<br>> Is it enough just to use the "-water spce" flag in pdb2gmx to make sure<br>> I am using SPC/E water, while genbox uses the default spc216.gro?<br>> <br>> <br>> Regards,<br>> -- <br>> Suman Chakrabarty<br>> <br>> <br>> -- <br>> This message has been scanned for viruses and<br>> dangerous content by MailScanner, and is<br>> believed to be clean.<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search 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 http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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