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<TD>Dear Dr. Xavier Periole,<br ><br >Thank you for guiding me through. I could solve the problem of setting up the system for minimization. However When started minimization run for 2000 steps with steepest descent , I encountered yet another problem. which is as follows ..<br ><br ><SPAN STYLE="font-weight: bold; font-style: italic;">Started Steepest Descents on node 0 Tue Dec 11 17:48:57 2007</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Removing pbc first time</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Done rmpbc</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Steepest Descents:</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;"> Tolerance (Fmax) = 1.00000e+01</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;"> Number of steps = 2000</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Grid: 4 x 5 x 4 cells</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">calc_bor: cg0=0, cg1=553, ncg=553</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">CG0[0]=0, CG1[0]=553</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">CG0[1]=0, CG1[1]=0</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">calc_bor: cg0=0, cg1=553, ncg=553</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">CG0[0]=0, CG1[0]=553</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">CG0[1]=0, CG1[1]=0</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Configuring nonbonded kernels...</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Testing AMD 3DNow support... not present.</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Testing ia32 SSE support... present.</SPAN><br style="font-weight: bold; font-style: italic;" ><br style="font-weight: bold; font-style: italic;" ><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;"> Step Time Lambda</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;"> 0 0.00000 0.00000</SPAN><br style="font-weight: bold; font-style: italic;" ><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">calc_bor: cg0=0, cg1=553, ncg=553</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">CG0[0]=0, CG1[0]=553</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">CG0[1]=0, CG1[1]=0</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">-------------------------------------------------------</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Program mdrun, VERSION 3.3</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Source code file: nsgrid.c, line: 226</SPAN><br style="font-weight: bold; font-style: italic;" ><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Range checking error:</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Explanation: During neighborsearching, we assign each particle to a grid</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">based on its coordinates. If your system contains collisions or parameter</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">errors that give particles very high velocities you might end up with some</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">put these on a grid, so this is usually where we detect those errors.</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Make sure your system is properly energy-minimized and that the potential</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">energy seems reasonable before trying again.</SPAN><br style="font-weight: bold; font-style: italic;" ><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Variable ci has value -2147483648. It should have been within [ 0 .. 80 ]</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Please report this to the mailing list (gmx-users@gromacs.org)<br ></SPAN><font size="2" face="Arial">-------------------------------------------------------</font><br >Now where do I go from here? Its asking me to energy minimize the system which what I am trying to do ! What is this ci value and why is it so high? Kindly help me I am once again stuck.<br ><br >regards<br >sharada<br > <br ><span style="font-weight: bold; font-style: italic;"></span><br ><br ><br ><strong><em>-- Original Message --</em></strong><br >From: "Xavier Periole" <X.Periole@rug.nl><br >To: Discussion list for GROMACS users <gmx-users@gromacs.org><br >Date: Tue, 11 Dec 2007 12:07:27 +0100<br >Subject: Re: Fw: Re: [gmx-users] Methanol SOL :Number of solvent molecules <br > = 0<br ><br ><br >in your agg2t.top you should replace the last line :<br >SOL XXX<br >by:<br >Methanol XXX<br ><br >which is the name of the molecule.<br ><br >You should also remove the angle definition in methanol.itp. Placing<br >a ";" at the beginning of the line is enough.<br ><br >XAvier<br ><br >On Tue, 11 Dec 2007 15:40:04 +0530 (IST)<br > sharada <sharada@ccmb.res.in> wrote:<br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> Dear Mark Abraham,<br >> I have changed MeoH to SOL in .gro and .itp files and also changed the <br >>#include line to "methanol.itp"<br >> It now seemed to have written the solvent molecules in the top file with SOL <br >>as the name with atom types of methanol. <br >> When I ran grompp program as following I get the error as shown below: I am <br >>also attaching the .gro,.itp,.top files. for information. Did I miss out <br >>anything ? <br >> grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr<br >> [asd@ccmb Aggregates]$ grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o <br >>agg2_em.tpr<br >> <br >> Option Type Value Description<br >> ------------------------------------------------------<br >> -[no]h bool no Print help info and quit<br >> -[no]X bool no Use dialog box GUI to edit command line options<br >> -nice int 0 Set the nicelevel<br >> -[no]v bool yes Be loud and noisy<br >> -time real -1 Take frame at or first after this time.<br >> -np int 1 Generate statusfile for # nodes<br >> -[no]shuffle bool no Shuffle molecules over nodes<br >> -[no]sort bool no Sort molecules according to X coordinate<br >> creating statusfile for 1 node...<br >> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#<br >> checking input for internal consistency...<br >> calling /lib/cpp...<br >> processing topology...<br >> Generated 141 of the 1176 non-bonded parameter combinations<br >> Excluding 3 bonded neighbours for Protein 1<br >> Cleaning up temporary file grompp5RBSRX<br >> -------------------------------------------------------<br >> Program grompp, VERSION 3.3<br >> Source code file: toppush.c, line: 1264<br >>Fatal error:<br >> No such moleculetype SOL<br >> -------------------------------------------------------<br >> I never prefer working in root as I know the problems. Thanks for <br >> suggesting. I needed to change the methanol.itp and methanol216.gro which <br >>could be possible only through root. <br >> regards<br >> sharada <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br >> <br ><br >-----------------------------------------------------<br >XAvier Periole - PhD<br ><br >NMR & Molecular Dynamics Group<br >University of Groningen<br >The Netherlands<br >http://md.chem.rug.nl/~periole<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>
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