<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt">Hi, <br>Thanks for the reply.<br>I converted the .dcd file to .trr format using the catdcd program. I used the command " g_covar -f TOTAL_50MS.trr -s CG_TNF.pdb -n new.ndx -o eigenval.xvg -v eigenvec.trr" to run and getting the error as follows:<br>------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>WARNING: masses will be determined based on residue and atom names,<br> this can deviate from the real mass of the atom type<br>Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat<br>Warning double different entries ASN ND 16.0227
and 144.24 on line 134 in file atommass.dat<br>Using last entry (16.0227)<br>Warning double different entries GLN NE 16.0227 and 20.1797 on line 140 in file atommass.dat<br>Using last entry (16.0227)<br>Warning double different entries HISA NE 14.0067 and 16.0227 on line 144 in file atommass.dat<br>Using last entry (14.0067)<br>Warning double different entries HISB ND 14.0067 and 16.0227 on line 145 in file atommass.dat<br>Using last entry (14.0067)<br>Warning double identical entries for HIS1 NE 14.0067 on line 146 in file atommass.dat<br>Entries in atommass.dat: 173<br>WARNING: vdwradii will be determined based on residue and atom names,<br> this can deviate from the real mass of the atom type<br>Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat<br>Entries in vdwradii.dat: 28<br>Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat<br>Entries in dgsolv.dat:
7<br>Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat<br>Entries in electroneg.dat: 71<br>Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat<br>Entries in elements.dat: 218<br><br>Choose a group for the least squares fit<br>Group 0 ( System) has 45 elements<br>Group 1 ( TA) has 15 elements<br>Group 2 ( TB) has 15 elements<br>Group 3 ( TC) has 15 elements<br>Group 4 (a_15_a_30_a_45) has 3 elements<br>Select a group: 0<br>Selected 0: 'System'<br><br>Choose a group for the covariance
analysis<br>Group 0 ( System) has 45 elements<br>Group 1 ( TA) has 15 elements<br>Group 2 ( TB) has 15 elements<br>Group 3 ( TC) has 15 elements<br>Group 4 (a_15_a_30_a_45) has 3 elements<br>Select a group: 0<br>Selected 0: 'System'<br><br>Note: the fit and analysis group are identical,<br> while the fit is mass weighted and the analysis is not.<br> Making the fit non mass weighted.<br><br>Calculating the average structure ...<br>Segmentation
fault<br>----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br><div> I also edited the aminoacids.dat file by giving the CG Beads names there. Do I need to incorporate any other change?<br><br>Regards, <br></div><div><font color="#0000bf" size="4"></font> </div><div style="color: rgb(0, 0, 191);"><strong>Anirban Ghosh</strong></div><div style="color: rgb(0, 0, 191);"><strong>Grade Based Engineer<br>Bioinformatics Team<br>Centre for Development of Advanced Computing (C-DAC)<br>Pune, India<br></strong></div><div><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> "gmx-users-request@gromacs.org"
<gmx-users-request@gromacs.org><br><b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org<br><b><span style="font-weight: bold;">Sent:</span></b> Wednesday, 15 April, 2009 9:05:48 PM<br><b><span style="font-weight: bold;">Subject:</span></b> gmx-users Digest, Vol 60, Issue 89<br></font><br>Send gmx-users mailing list submissions to<br> <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>or, via email, send a message with subject or body 'help' to<br> <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br><br>You can reach the person managing the list
at<br> <a ymailto="mailto:gmx-users-owner@gromacs.org" href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br><br><br>Today's Topics:<br><br> 1. Re: Implicit Solvent System - Energy Minimization (Mark Abraham)<br> 2. g_covar Segmentation fault (Anirban Ghosh)<br> 3. Re: g_covar Segmentation fault (Mark Abraham)<br> 4. Re: g_covar Segmentation fault (Nicolas)<br> 5. Topologies and charges for large organic ligands (Dean Cuebas)<br> 6. Re: Topologies and charges for large organic ligands<br> (Ran Friedman)<br> 7. Problem with grompp? (Hoof, B. van)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Wed, 15 Apr 2009 19:55:26 +1000<br>From: Mark Abraham <<a
ymailto="mailto:Mark.Abraham@anu.edu.au" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>Subject: Re: [gmx-users] Implicit Solvent System - Energy Minimization<br>To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a ymailto="mailto:49E5AF0E.6020503@anu.edu.au" href="mailto:49E5AF0E.6020503@anu.edu.au">49E5AF0E.6020503@anu.edu.au</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Grace Tang wrote:<br>> Hello All,<br>> <br>> I am doing energy minimization on a protein crystal structure to relax <br>> it. Afterwards, I plan to run md simulation with implicit solvent. I <br>> am new at this and have many questions.<br>> 1. Should the implicit solvent conditions be enabled when I run the <br>> energy minimization?<br><br>No - while GROMACS has some vestiges
in the user interface of an earlier <br>attempt to implement implicit solvation simulations, these will not <br>functional until at least version 4.1.<br><br>> 2. What minimum potential energy should I expect (i know that when <br>> explicit water is present, the energy often reaches -10E5 or -10E6)<br><br>Negative, and vaguely proportional to the number of atoms.<br><br>> 3. What kind of emtol is appropriate? Is it better to set it high so <br>> that the system converges, or is it okay if machine precision is reached. <br><br>It's pretty much irrelevant for preparing a system for MD. You'll have <br>to equilibrate it later, and the value of an EM step is merely relieving <br>any bad atom-atom contacts before they turn into huge accelerations. If <br>the equilibration doesn't crash, you did enough EM.<br><br>Mark<br><br>> Below are 2 example runs I did with implicit_solvent = no<br>> When I decreased the step size, the
system did not converge anymore. I <br>> was wondering if this was due to chance, precision issues (I am using <br>> single precision), or perhaps the emstep = 0.1 was reaching a nearby <br>> minimum and 0.01 was reaching the local minimum. Note, maximum force <br>> gets rather large when convergence is to machine precision.<br>> <br>> emtol = 1000<br>> emstep = 0.1<br>> Steepest Descents converged to Fmax < 1000 in 29 steps<br>> Potential Energy = -4.9613008e+003<br>> Maximum force = 6.4596338e+002 on atom 235<br>> Norm of force = 1.0625026e+002<br>> <br>> emtol = 1000<br>> emstep = 0.01<br>> Steepest
Descents converged to machine precision in 25 steps,<br>> but did not reach the requested Fmax < 1000.<br>> Potential Energy = -3.9642480e+003<br>> Maximum force = 5.1200122e+003 on atom 416<br>> Norm of force = 3.6602789e+002<br>> <br>> Any advice is greatly appreciated. Much thanks!<br>> - Grace<br>> <br>> <br>> ------------------------------------------------------------------------<br>> <br>> _______________________________________________<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>>
Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br><br><br>------------------------------<br><br>Message: 2<br>Date: Wed, 15 Apr 2009 18:12:32 +0530 (IST)<br>From: Anirban Ghosh <<a ymailto="mailto:anirbanz83@yahoo.co.in" href="mailto:anirbanz83@yahoo.co.in">anirbanz83@yahoo.co.in</a>><br>Subject: [gmx-users] g_covar Segmentation fault<br>To: GROMACS <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a ymailto="mailto:1093.26419.qm@web8504.mail.in.yahoo.com"
href="mailto:1093.26419.qm@web8504.mail.in.yahoo.com">1093.26419.qm@web8504.mail.in.yahoo.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>Hi ALL,<br><br>I have a system of beads with which I ran a CGMD (coarse grained MD) using NAMD. Now I want to do a PCA analysis of this system using GROMACS. So I converted the trajectory in .trr format and made an index file of the entire system (45 beads). But now when I try to run g_covar using the group consisting the entire system, for least square fit and covariance analysis, it is giving Segmentation Fault. Am I doing anything wrong. Any suggestion is welcome.<br><br>Regards,<br><br> <br> <br>Anirban Ghosh<br>Grade Based Engineer<br>Bioinformatics Team<br>Centre for Development of Advanced Computing (C-DAC)<br>Pune, India<br><br><br> Add more friends to your messenger and enjoy! Go to <a href="http://messenger.yahoo.com/invite/"
target="_blank">http://messenger.yahoo.com/invite/</a><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20090415/4b881e11/attachment-0001.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/attachments/20090415/4b881e11/attachment-0001.html</a><br><br>------------------------------<br><br>Message: 3<br>Date: Wed, 15 Apr 2009 22:48:51 +1000<br>From: Mark Abraham <<a ymailto="mailto:Mark.Abraham@anu.edu.au" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>Subject: Re: [gmx-users] g_covar Segmentation fault<br>To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a ymailto="mailto:49E5D7B3.3030305@anu.edu.au"
href="mailto:49E5D7B3.3030305@anu.edu.au">49E5D7B3.3030305@anu.edu.au</a>><br>Content-Type: text/plain; charset=UTF-8; format=flowed<br><br>Anirban Ghosh wrote:<br>> Hi ALL,<br>> <br>> I have a system of beads with which I ran a CGMD (coarse grained MD) <br>> using NAMD. Now I want to do a PCA analysis of this system using <br>> GROMACS. So I converted the trajectory in .trr format and made an index <br>> file of the entire system (45 beads). But now when I try to run g_covar <br>> using the group consisting the entire system, for least square fit and <br>> covariance analysis, it is giving Segmentation Fault. Am I doing <br>> anything wrong. Any suggestion is welcome.<br><br>Yes you're doing something wrong, but if you don't tell us at least your <br>command line and your full output, how might we be expected to help? :-)<br><br>Mark<br><br><br>------------------------------<br><br>Message: 4<br>Date: Wed, 15 Apr 2009
15:02:55 +0200<br>From: Nicolas <<a ymailto="mailto:nsapay@ucalgary.ca" href="mailto:nsapay@ucalgary.ca">nsapay@ucalgary.ca</a>><br>Subject: Re: [gmx-users] g_covar Segmentation fault<br>To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a ymailto="mailto:49E5DAFF.2000705@ucalgary.ca" href="mailto:49E5DAFF.2000705@ucalgary.ca">49E5DAFF.2000705@ucalgary.ca</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>Anirban Ghosh a écrit :<br>> Hi ALL,<br>><br>> I have a system of beads with which I ran a CGMD (coarse grained MD) <br>> using NAMD. Now I want to do a PCA analysis of this system using <br>> GROMACS. So I converted the trajectory in .trr format<br>Convert a dcd file into a trr file is not that straightforward. How did <br>you do that?<br>> and made an index file of the entire system (45 beads). But
now when I <br>> try to run g_covar using the group consisting the entire system, for <br>> least square fit and covariance analysis, it is giving Segmentation <br>> Fault. Am I doing anything wrong. Any suggestion is welcome.<br>You probably also need a tpr file. To create it, you need the parameters <br>of your force field (in Gromacs format), the topology of each molecule <br>you've got in your system (still in Gromacs format) and to run grompp. <br>Depending on the original format of your force field, in can be quite <br>difficult to do the file format conversion.<br><br>Hope that helps...<br>Nicolas<br>><br>> Regards,<br>> <br>> <br>> *Anirban Ghosh*<br>> *Grade Based Engineer<br>> Bioinformatics Team<br>> Centre for Development of Advanced Computing (C-DAC)<br>> Pune, India<br>> *<br>><br>><br>> ------------------------------------------------------------------------<br>> Add
more friends to your messenger and enjoy! Invite them now. <br>> <<a href="http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/" target="_blank">http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/</a>> <br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to <a
ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br><br>-------------- next part --------------<br>A non-text attachment was scrubbed...<br>Name: nsapay.vcf<br>Type: text/x-vcard<br>Size: 322 bytes<br>Desc: not available<br>Url : <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20090415/543052fd/nsapay-0001.vcf" target="_blank">http://www.gromacs.org/pipermail/gmx-users/attachments/20090415/543052fd/nsapay-0001.vcf</a><br><br>------------------------------<br><br>Message: 5<br>Date: Wed, 15 Apr 2009 10:03:40 -0500<br>From: Dean Cuebas <<a ymailto="mailto:deancuebas@missouristate.edu" href="mailto:deancuebas@missouristate.edu">deancuebas@missouristate.edu</a>><br>Subject: [gmx-users] Topologies and charges for
large organic ligands<br>To: <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <C60B617C.28718%<a ymailto="mailto:deancuebas@missouristate.edu" href="mailto:deancuebas@missouristate.edu">deancuebas@missouristate.edu</a>><br>Content-Type: text/plain; charset="US-ASCII"<br><br>Dear colleagues,<br><br>In 53a6, the topology and charges for (NAD+) nicotinamide adenine<br>dinucleotide are present (listed as NADH, 52 atoms) in polar hydrogen form<br>(without aromatic hydrogens).<br><br>Is there anyone who can tell me how such a molecule was charge group<br>parameterized? (with sufficient certainty to be included in the ff).<br><br>Please understand that I am not asking how to use the NAD topology that's<br>provided.<br><br>I've read that prodrg is a "good starting point" for parametrizing a ligand,<br>but what is the path to "improving" such a ligand from that
starting point?<br>(the provided topology for NAD+ in the ff shows 17 charge groups with<br>an average of 3-4 atoms per charge group, whereas prodrg gives only 11<br>charge groups.)<br><br>I'm not concerned about angles and dihedrals, since that is pretty<br>painless... it's the charge groups that I'm concerned about.<br><br>In a nutshell, who and how was the final NAD+ parameters decided upon??<br>Does anyone know this?? Is it simply chemical intuition of estimated<br>charges that reproduce the dipole of the moiety (like an adenine ring), and<br>the charge groups contain the minimum number of atoms that reflect this?<br><br>Is there an algorithm to generating "improved" charge groups?<br><br>I ask these questions because my ligands are large organics... MW 800 and<br>greater.<br><br>Thanks for any and all help in this regard.<br><br>-- <br>Dr. Dean Cuebas, Associate Prof of Chemistry<br><a ymailto="mailto:deancuebas@smsu.edu"
href="mailto:deancuebas@smsu.edu">deancuebas@smsu.edu</a>, Ph 417-836-8567 FAX 417-836-5507<br>Dept. of Chemistry, Southwest Missouri State University<br>Springfield, Missouri 65804<br><br><br><br><br><br>------------------------------<br><br>Message: 6<br>Date: Wed, 15 Apr 2009 17:26:50 +0200<br>From: Ran Friedman <<a ymailto="mailto:r.friedman@bioc.uzh.ch" href="mailto:r.friedman@bioc.uzh.ch">r.friedman@bioc.uzh.ch</a>><br>Subject: Re: [gmx-users] Topologies and charges for large organic<br> ligands<br>To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a ymailto="mailto:49E5FCBA.10606@bioc.uzh.ch" href="mailto:49E5FCBA.10606@bioc.uzh.ch">49E5FCBA.10606@bioc.uzh.ch</a>><br>Content-Type: text/plain; charset=ISO-8859-1<br><br>Hi,<br><br>The answer is (or should be) in:<br><br>@article{Oostenbrink2004,<br>
Author = {Oostenbrink, C. and Villa, A. and Mark, A. E. and Van<br>Gunsteren, W. F.},<br> Title = {A biomolecular force field based on the free enthalpy of<br>hydration and solvation: The GROMOS force-field parameter sets 53A5 and<br>53A6},<br> Journal = {J. Comput. Chem.},<br> Volume = {25},<br> Pages = {1656-1676},<br> Year = {2004} }<br><br>Good luck,<br>Ran.<br><br>Dean Cuebas wrote:<br>> Dear colleagues,<br>><br>> In 53a6, the topology and charges for (NAD+) nicotinamide adenine<br>> dinucleotide are present (listed as NADH, 52 atoms) in polar hydrogen form<br>> (without aromatic hydrogens).<br>><br>> Is there anyone who can tell me how such a molecule was charge group<br>> parameterized? (with sufficient certainty to be included in the ff).<br>><br>> Please understand that I am not asking how to use the NAD topology that's<br>> provided.<br>><br>> I've read that prodrg is a
"good starting point" for parametrizing a ligand,<br>> but what is the path to "improving" such a ligand from that starting point?<br>> (the provided topology for NAD+ in the ff shows 17 charge groups with<br>> an average of 3-4 atoms per charge group, whereas prodrg gives only 11<br>> charge groups.)<br>><br>> I'm not concerned about angles and dihedrals, since that is pretty<br>> painless... it's the charge groups that I'm concerned about.<br>><br>> In a nutshell, who and how was the final NAD+ parameters decided upon??<br>> Does anyone know this?? Is it simply chemical intuition of estimated<br>> charges that reproduce the dipole of the moiety (like an adenine ring), and<br>> the charge groups contain the minimum number of atoms that reflect this?<br>><br>> Is there an algorithm to generating "improved" charge groups?<br>><br>> I ask these questions because my ligands are large organics... MW 800
and<br>> greater.<br>><br>> Thanks for any and all help in this regard.<br>><br>> <br><br><br><br>------------------------------<br><br>Message: 7<br>Date: Wed, 15 Apr 2009 17:25:15 +0200<br>From: "Hoof, B. van" <<a ymailto="mailto:B.v.Hoof@tue.nl" href="mailto:B.v.Hoof@tue.nl">B.v.Hoof@tue.nl</a>><br>Subject: [gmx-users] Problem with grompp?<br>To: "<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <<a ymailto="mailto:C33253DAA8B7D24E9523B6F1DF162F5A01A73BE9BCDE@EXCHANGE10.campus.tue.nl" href="mailto:C33253DAA8B7D24E9523B6F1DF162F5A01A73BE9BCDE@EXCHANGE10.campus.tue.nl">C33253DAA8B7D24E9523B6F1DF162F5A01A73BE9BCDE@EXCHANGE10.campus.tue.nl</a>><br> <br>Content-Type: text/plain;
charset="us-ascii"<br><br>Hi everyone,<br><br>Since I am a new user of Gromacs, this problem is probably rather trivial, but I hope one of you would like to help me nonetheless. I have created a starting structure in a not very optimal situation, which I have then minimized. To continue, I would like to equilibrate the system further using leap-frog MD. To do so, I have used grompp in the following way:<br>grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10<br><br>This creates the following mdout.mdp: see attachment<br><br>Now as far as I can see, using the command `mdrun -v -c md_run.gro' should result in performing a 1,000,000 iteration md simulation of this system. However, when I issue that command, instead what I get is this:<br>>>><br> :-) G R O M A C S (-:<br><br>
Good ROcking Metal Altar for Chronical Sinners<br><br> :-) VERSION 4.0.4 (-:<br><br><br>[...]<br><br> :-) mdrun (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br>[...]<br><br>Getting Loaded...<br>Reading file topol.tpr, VERSION 4.0.4 (single precision)<br>Loaded with Money<br><br>Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+01<br> Number of steps = 10000<br>Step= 1, Dmax= 1.0e-02 nm, Epot= 1.23314e+20 Fmax= 2.04950e+19, atom= 11163<br>Step= 2, Dmax= 1.2e-02 nm, Epot= 5.22616e+17
Fmax= 2.22256e+20, atom= 10863<br>Step= 3, Dmax= 1.4e-02 nm, Epot= 1.46382e+17 Fmax= 7.52962e+17, atom= 10593<br>Step= 4, Dmax= 1.7e-02 nm, Epot= 1.21703e+17 Fmax= 3.72098e+16, atom= 10331<br>Step= 5, Dmax= 2.1e-02 nm, Epot= 2.22862e+16 Fmax= 4.87326e+18, atom= 10857<br>Step= 6, Dmax= 2.5e-02 nm, Epot= 1.09032e+16 Fmax= 4.39937e+15, atom= 15106<br>Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81517e+15 Fmax= 6.07049e+14, atom= 15230<br>Step= 8, Dmax= 3.6e-02 nm, Epot= 2.84750e+14 Fmax= 9.82848e+14, atom= 14675<br>Step= 9, Dmax= 4.3e-02 nm, Epot= 2.33131e+14 Fmax= 2.39469e+13, atom= 11419<br>Step= 10, Dmax= 5.2e-02 nm, Epot= 7.23189e+12 Fmax= 2.72305e+14, atom= 14565<br>Step= 11, Dmax= 6.2e-02 nm, Epot= 3.19510e+12 Fmax= 4.82192e+12, atom= 10638<br>Step= 13, Dmax= 3.7e-02 nm, Epot= 1.82616e+12
Fmax= 1.11184e+13, atom= 11929<br>[... etc.....]<br><<<<br><br>This is a minimization using the steepest descent algorithm. What am I doing wrong here?<br><br>Thank you in advance for your kind help!<br><br>Greetings,<br>Bram van Hoof<br><br><br><br><br>-------------- next part --------------<br>A non-text attachment was scrubbed...<br>Name: mdout.mdp<br>Type: application/octet-stream<br>Size: 9904 bytes<br>Desc: mdout.mdp<br>Url : <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20090415/109a0d76/mdout.obj" target="_blank">http://www.gromacs.org/pipermail/gmx-users/attachments/20090415/109a0d76/mdout.obj</a><br><br>------------------------------<br><br>_______________________________________________<br>gmx-users mailing list<br><a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users"
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