<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY><br >Thanks for the reply.<br ><br >I am sorry about the typo mistake, it is 45a3 forcefield that I am working with & that I choose by giving the option 3 in pdb2gmx. So with PME the epsilon_r value has to be mentioned ?.Are the different forcefields 43a1,45a3 etc have to be used with different sets <font face="Arial" size="2"></font> of rvdw, rcoulomb & rlist ? In that case what would be the set of values if I am working with 45a3 forcefield with PME option ? How do I give correction term for dispersion otherwise? Are the methanol .gro and itp files that I am taking the right ones ? <br ><br >regards,<br >sharada<br ><br ><font face="Arial" size="2"><br ><TABLE STYLE="PADDING-LEFT: 5px; BORDER-BOTTOM-COLOR: blue; BORDER-LEFT: blue 1px solid; BORDER-TOP-COLOR: blue; BORDER-RIGHT-COLOR: blue"><tbody><TR><TD><strong><em>-- Original Message --</em></strong><br >From: "Justin A. Lemkul" <jalemkul@vt.edu><br >To: "Gromacs Users' List" <gmx-users@gromacs.org><br >Date: Sat, 31 Jan 2009 07:35:42 -0500<br >Subject: Re: [gmx-users] Melittin in methanol...<br ><br ><br ><br >sharada wrote:<br >> Hello Justin,<br >> <br >> Thanks for the reply . I apologise for the repeat mail. The parameters <br >> are for ffG43a3 forcefield. Yes I am using the default electrotatics <br >> cutoff values as an initial run. I would change to PME method as you <br >> say. However I was wondering If r_epsilon value equals to 66 contributes <br >> to a change in the simulation or this value holds good only if reaction <br >> field is on ? <br >> <br ><br >I have never heard of 43a3, do you mean 43a1, or perhaps 45a3? Better be sure <br >about what you're using so you get the .mdp options right. Use PME, and make <br >sure your values of rlist, rcoulomb, and rvdw are for use with that particular <br >parameter set (rvdw = 0.8 is particularly troubling, especially in the absence <br >of any dispersion correction).<br ><br >With cut-off, the epsilon_r parameter is probably meaningless.<br ><br >-Justin<br ><br >> sharada<br >> <br >> <br >> */-- Original Message --/*<br >> From: "Justin A. Lemkul" <jalemkul@vt.edu><br >> To: Discussion list for GROMACS users <gmx-users@gromacs.org><br >> Date: Sat, 31 Jan 2009 00:42:36 -0500<br >> Subject: Re: [gmx-users] Melittin in methanol...<br >> <br >> <br >> <br >> sharada wrote:<br >> <br >> > rlist = 0.5<br >> > rcoulomb = 1.4<br >> > rvdw = 0.8<br >> <br >> You are using cut-off electrostatics by default, so you are probably <br >> getting<br >> some bad artifacts (use PME instead). Also, the values of rlist, <br >> rcoulomb, and<br >> rvdw you are using do not correspond to those for which the Gromos96 <br >> force field<br >> was derived. These make no sense. Refer to the original literature for<br >> whichever parameter set you decided to use.<br >> <br >> -Justin<br >> <br >> <br >> -- <br >> ========================================<br >> <br >> Justin A. Lemkul<br >> Graduate Research Assistant<br >> Department of Biochemistry<br >> Virginia Tech<br >> Blacksburg, VA<br >> jalemkul[at]vt.edu | (540) 231-9080<br >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<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 ><br >-- <br >========================================<br ><br >Justin A. Lemkul<br >Graduate Research Assistant<br >Department of Biochemistry<br >Virginia Tech<br >Blacksburg, VA<br >jalemkul[at]vt.edu | (540) 231-9080<br >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<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 ></TD></TR></tbody></TABLE></font></BODY></HTML>