<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><p>Hi,</p><p>Thankyou for the prompt response. I am using the methanol box provided along with gromacs software<br >This is the itp file I am using ... <br ><br ><strong>usr/local/gromacs/share/gromacs/top$ more methanol.itp<br >#ifndef _FF_GROMOS96</strong></p><p><strong>[ atomtypes ]<br >; type mass charge ptype c6 c12<br > OMET 15.999 -0.69 A 2.6169e-3 2.5231e-6<br > OW 15.999 -0.82 A 2.6170e-3 2.6330e-6<br > CMET 15.035 0.29 A 8.8758e-3 17.8426e-6<br > H 1.008 0.4 A 0.0 0.0<br > HW 1.008 0.41 A 0.0 0.0<br >#endif</strong></p><p><strong>[ moleculetype ]<br >; name nrexcl<br >Methanol 2</strong></p><p><strong>[ atoms ]<br >; nr type resnr residu atom cgnr charge mass<br >#ifdef _FF_GROMOS96<br >1 CMET 1 MeOH Me1 1 0.176 15.035 <br >2 OMET 1 MeOH O2 1 -0.574 15.999 <br >3 H 1 MeOH H3 1 0.398 1.008 <br >#else<br >1 CMET 1 MeOH Me1 1 0.29 15.035<br >2 OMET 1 MeOH O2 1 -0.69 15.999<br >3 H 1 MeOH H3 1 0.40 1.008<br >#endif</strong></p><p><strong>[ bonds ]<br >; ai aj funct c0 c1<br >1 2 1 0.13600 376560.<br >2 3 1 0.10000 313800.</strong></p><p><strong>[ angles ]<br >; ai aj ak funct c0 c1<br > 1 2 3 1 108.53 397.5<br ><br ></strong>I would try using the new force field. <br ><br >sharada<br ><br ><br ><br ><br ></p><font face="Arial" size="2"><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><br ><strong><em>-- Original Message --</em></strong><br >From: "Justin A. Lemkul" <jalemkul@vt.edu><br >To: Discussion list for GROMACS users <gmx-users@gromacs.org><br >Date: Thu, 29 Jan 2009 08:47:34 -0500<br >Subject: Re: [gmx-users] Melittin in Methanol.......<br ><br ><br ><br >sharada wrote:<br >> Hello,<br >> <br >> I am doing a simulation of melittin molecule in methanol box for 3 ns. <br >> I am finding that it is unfolding very rapidly and is behaving more like <br >> in water. <br >> Melittin behaviour in water, methanol and also in lipids is well <br >> documented and known since quite some time. I am using the <br >> methanol216.gro provided along with gromacs software. I am using ffG43a3 <br >> force field. The density of methanol is around 771.238 g/l. The <br >> backbone rmsd shoots up to 0.5nm immediatly after 500 ps which <br >> indicates that it is unfolding. I have no clue why it is behaving in <br >> this manner. Melittin unfolds in water like this but not in methanol. <br >> Can any one tell me where I am going wrong. Any insight in this <br >> direction is welcome.<br >> <br ><br >Several possibilities. What parameters are you using for methanol? Did you <br >derive them yourself, or did you obtain them from somewhere else?<br ><br >Also, you can consider using a newer (improved) force field, like Gromos96 53a6.<br ><br >-Justin<br ><br >> Thankyou in advance<br >> <br >> sharada<br >> <br >> <br >> <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 >-- <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>