<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class='hmmessage'><div style="text-align: left;">I guess you are using soft-core interactions.<br>In that case there are more terms in dV/dl, see eq. 4.120 in the manual.<br><br>Berk.<br><br></div><br><hr id="stopSpelling">> Date: Mon, 14 Apr 2008 18:13:32 +0200<br>> From: reich@mpikg.mpg.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] VdW and Coulomb SR contribution to dVdl in thermodynamic integration<br>> <br>> Dear Gromacs-users,<br>> <br>> I have been doing a test thermodynamic integration for the conversion of<br>> methanol into a dummy molecule in water. I have been interested in the<br>> contribution of the VdW and Coulomb short range interaction to dVdl.<br>> According to equations 4.108 and 4.104, at lambda=0 (the methanol-state)<br>> the contributions should be the negative Lennard-Jones and Coulomb short<br>> range interaction energies between methanol and the surrounding water. I<br>> have been calculating the interaction energies with g_energy (choosing<br>> LJ-SR:methanol-rest and Coul-SR:methanol-rest as options). For example for<br>> a particular step in my trajectory I get<br>> <br>> -7.954321 kJ/mol for the Lennard-Jones interaction<br>> <br>> and -56.966656 kJ/mol for the Coulomb intercation between methanol and water.<br>> <br>> So the contribution of the combined interactions to dVdl should be<br>> <br>> 64.921 kJ/mol<br>> <br>> <br>> I have, however, also used the option sepdvdl with mdrun to get some<br>> detailed information on dVdl during the simulation.<br>> The line from the log-file giving me the contribution of Lennard-Jones and<br>> Coulomb short range interactions for the simulation step in question is:<br>> <br>> VdW and Coulomb SR particle-p. V -1.49467e+04 dVdl 1.01145e+03<br>> <br>> So the simulation output gives me a result that is two magnitudes greater<br>> than what I calculated! Is there anything wrong with my reasoning or do<br>> you have any other clue why I end up with two different results?<br>> <br>> <br>> Thanks<br>> <br>> Luther<br>> <br>> <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>
</html>