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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 >Methanol optimization:<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;" ><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 is 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. Furthermore, when I minimized the same peptide in SPC216 water box of 1108 water molecules for 2000 steps this error did not appear. When I compared the md.log files in both the cases I found that in case of water optimization of SPC water was enabled where as this line for methanol was missing which should mean that the energies are shooting off scale is that right ? Should I optimize my system in vacuo before simmulating in methanol? <br ><br ><br >Water optimization:<br ><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">{Generated table with 500 data points for 1-4 LJ12.</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Tabscale = 500 points/nm</SPAN><br style="font-weight: bold;" ><br style="font-weight: bold;" ><SPAN STYLE="font-style: italic; font-weight: bold;">Enabling SPC water optimization for 1108 molecules</SPAN><SPAN STYLE="font-weight: bold;">.</SPAN><br style="font-weight: bold;" ><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Initiating Steepest Descents</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Center of mass motion removal mode is Linear</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">We have the following groups for center of mass motion removal:</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 0: rest, initial mass: 3396</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Started Steepest Descents on node 0 Wed Dec 12 15:52:11 2007</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Removing pbc first time</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Done rmpbc</SPAN><br style="font-weight: bold;" ><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Steepest Descents:</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> Tolerance (Fmax) = 1.00000e+01</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> Number of steps = 2000</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Going to use C-settle (1108 waters)</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Grid: 4 x 5 x 4 cells}</SPAN><br ><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 >> 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 >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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</font>_______________________________________________<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</TD>
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