[gmx-users] reaction field kappa and ionic strength
dear all, there are errors in the code regarding 1) the equation for kappa, which is used for the reaction field method; and 2) in the calculation of the ionic strength. 1) in rf_util.c kappa is calculated as *kappa = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp)); but the factor 2 in the square root is only correct if the sum in the ionic strength I is actually divided by 2, which it isn't. so the factor 2 should be omitted. 2) in force.c the ionic strength is (among others) calculated by summing the absolute values instead of the squares of the charges. zsq += fabs(q); this is only correct for monovalent charge groups. @developers: these errors have been remarked previously on the mailing list. as it is not mentioned in the bugzilla, i thought i can bring it up again... can you correct this in the code for the next version please? thanks. best regards, daniela -- Daniela S. Mueller Biologist (Dipl. Biol.) Molecular Dynamics (MD) Groningen Biomolecular Sciences and Biotechnology Institute (GBB) MD group website: http://www.rug.nl/gbb/md Daniela Mueller Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Tel.: +31 (0)50 3634327 Fax.: +31 (0)50 3634398 e-mail: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] beta dihedral potential for nucleic acid backbone missing in force field file
dear all, in the force field file for residue types ffG53a6.rtp, one of the two potentials for the so-called "beta" dihedral angle for the nucleic acid backbone atoms P-O5'-C5'-C4' is missing. this dihedral potential term is indicated in the article published with the GROMOS force field 45A4 by Soares et al. 2005 in the Journal of Computational Chemistry Vol. 26, No.7, pp. 725-737. the parameter set 45A4 is dedicated to nucleic acids, and if i see this correctly, it was incorporated into the 53A6 force field without further changes. therefore i suppose this potential was forgotten and should be included in the force field. best regards, daniela -- Daniela S. Mueller Biologist (Dipl. Biol.) Molecular Dynamics (MD) Groningen Biomolecular Sciences and Biotechnology Institute (GBB) MD group website: http://www.rug.nl/gbb/md Postal address: Daniela Mueller Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Tel.: +31 (0)50 3634327 Fax.: +31 (0)50 3634398 e-mail: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with dimer simulation !
hi cw, using trjconv -pbc nojump should remove the jumps. then you can analyse interactions between different chains, while it doesn't matter for the analysis where they diffuse. daniela Kay Gottschalk wrote: try - cluster, and then as cluster group protein. Kay. On Sep 9, 2006, at 11:09 AM, C.W. Liang wrote: hi, all user: i performed the dimer simulation, and want to realize the interaction between two peptides. but frequently, i encountered this kind of problem: sometimes peptides moved out of the box, and sometimes they jumped back. i have tried so many way to pull them back with trjconv command, but still cause some unexpected problem. for example, peptides break to many parts ( with -pbc whole ) or diffuse out of box gradually ( with -pbc nojump ) with -ur or -center still not the trajectory i really want. i think maybe there are some tricks to perform. any suggestions for me ? thanks sooo much! -- Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. -- Daniela S. Mueller Biologist (Dipl. Biol.) __ - Molecular Dynamics Group, UQ - Address: School of Molecular and Microbial Sciences (SMMS) Chemistry Building (#68) University of Queensland Qld 4072, Brisbane Australia Phone: +61-7-33653732 Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm ** - MD group, RuG - Address: Molecular Dynamics Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Website: http://www.rug.nl/gbb/md __ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx problem
hi, that's because your input-file was already in gro-format. use a pdb-file and you will get the options. daniela On Tue, 2006-03-28 at 11:30 +0800, Rongliang Wu wrote: > Hello, gmx-users， > when i added the appropriate terms to the .tdb file, i used "pdb2gmx -f > .gro -ter" it didnot tell me to select the terminal groups, and the generated > .top file has no connection between residues and the terminal groups are not > changed. why? > > Regards > > Thanks > > > Rongliang Wu > [EMAIL PROTECTED] > 2006-03-28 -- Daniela S. Mueller biologist (Diplom, German degree) __ - Molecular Dynamics Group, UQ - Address: School of Molecular and Microbial Sciences (SMMS) Chemistry Building (#68) University of Queensland Qld 4072, Brisbane Australia Phone: +61-7-33653732 Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm ** - MD group, RuG - Address: Molecular Dynamics Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Website: http://www.rug.nl/gbb/md __ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_hbond question
try g_hbond -g! daniela On Wed, 2006-03-22 at 06:15 -0600, Moore, Jonathan (J) wrote: > Daniela, > > Thanks for that tip. It looks like that won't help me, though, because I > can't get it to write out the log file. > > Jonathan > > > Jonathan Moore, Ph.D. > Research and Engineering Sciences - New Products > Core R&D > The Dow Chemical Company > 1702 Building, Office 4E > Midland, MI 48674 USA > Phone: (989) 636-9765 > Fax: (989) 636-4019 > E Mail: [EMAIL PROTECTED] > > > -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of Daniela S. Mueller > Sent: Wednesday, March 22, 2006 12:23 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] g_hbond question > > > hi jonathan, > > the actually occuring hydrogen bonds are listed in the log-file. > > daniela > > > On Tue, 2006-03-21 at 14:56 -0800, Moore, Jonathan (J) wrote: > > I created a hydrogen bond map using g_hbond of version 3.3. The > > manual indicates that for the hbmap the "Ordering is identical to that > > in -hbn index file." However, in my case, the hbmap file contains 13 > > hydrogen bond indices, but the hbond.ndx file lists 20 sets of donors > > and acceptors. Why the mismatch? How do I know which hydrogen bonds > > are represented in the map? > > > > Thanks, > > Jonathan > > > > > > Jonathan Moore, Ph.D. > > Research and Engineering Sciences - New Products > > Core R&D > > The Dow Chemical Company > > 1702 Building, Office 4E > > Midland, MI 48674 USA > > Phone: (989) 636-9765 > > Fax: (989) 636-4019 > > E Mail: [EMAIL PROTECTED] > -- Daniela S. Mueller biologist (Diplom, German degree) __ - Molecular Dynamics Group, UQ - Address: School of Molecular and Microbial Sciences (SMMS) Chemistry Building (#68) University of Queensland Qld 4072, Brisbane Australia Phone: +61-7-33653732 Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm ** - MD group, RuG - Address: Molecular Dynamics Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Website: http://www.rug.nl/gbb/md __ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_hbond question
hi jonathan, the actually occuring hydrogen bonds are listed in the log-file. daniela On Tue, 2006-03-21 at 14:56 -0800, Moore, Jonathan (J) wrote: > I created a hydrogen bond map using g_hbond of version 3.3. The manual > indicates that for the hbmap the "Ordering is identical to that in -hbn index > file." However, in my case, the hbmap file contains 13 hydrogen bond > indices, but the hbond.ndx file lists 20 sets of donors and acceptors. Why > the mismatch? How do I know which hydrogen bonds are represented in the map? > > Thanks, > Jonathan > > > Jonathan Moore, Ph.D. > Research and Engineering Sciences - New Products > Core R&D > The Dow Chemical Company > 1702 Building, Office 4E > Midland, MI 48674 USA > Phone: (989) 636-9765 > Fax: (989) 636-4019 > E Mail: [EMAIL PROTECTED] -- Daniela S. Mueller biologist (Diplom, German degree) __ - Molecular Dynamics Group, UQ - Address: School of Molecular and Microbial Sciences (SMMS) Chemistry Building (#68) University of Queensland Qld 4072, Brisbane Australia Phone: +61-7-33653732 Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm ** - MD group, RuG - Address: Molecular Dynamics Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Website: http://www.rug.nl/gbb/md __ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Villin Benchmarks grompp error (Please Help)
hi arindam, run pdb2gmx first to generate a topology-file. it would contain a bit more than yours... best regards, daniela On Thu, 2006-03-09 at 13:11 -0600, Arindam Ganguly wrote: > Hi GROMACS users, > sorry please disregard the earlier message realised it was too long. > i am new to GROMACS. i have been trying to run the Villin Benchmarks > using the conf.gro, grompp.mdp and topol.top file provided with the > benchmark folder. i giving the grompp command as follows > > grompp -f grompp.mdp -c conf.pdb -p topol.top -o em.tpr > > and after that i get this message, > > Fatal error: > number of coordinates in coordinate file (conf.pdb , 9389) > does not match topology (topol.top, 0) > --- > > "The Candlelight Was Just Right" (Beastie Boys) > > After going through the GROMACS mailing list I realised this is a > classical mistake which everyone makes. that's fine, but even after > making the changes as pointed out by many users that check the number > of atoms in topol.top and conf.gro file i am still getting the same > error. > i am providing in the email conf.gro and the topol.top file. can > anyone of you plz suggest as to what is wrong. where i have to make > the changes > inorder for me to run the simulation.thanks. > the file are provided below. > > Arindam Ganguly > > conf.gro > VILLIN in water > 9389 > 1MET N1 2.185 2.903 2.012 -0.4460 -0.1439 0.3043 > last line of the conf.gro file > 3036SOLHW2 9389 4.069 1.007 3.359 0.8423 -0.6670 -0.9379 >5.02729 4.73973 4.10445 0.0 0.0 1.67574 0.0 > -1.67574 2.36986 > > topol.top file > [ system ] > ; Name > VILLIN in water > > [ molecules ] > ; Compound#mols > Protein 390 > SOL 8999 > > > -- Daniela S. Mueller biologist (Diplom, German degree) __ - Molecular Dynamics Group, UQ - Address: School of Molecular and Microbial Sciences (SMMS) Chemistry Building (#68) University of Queensland Qld 4072, Brisbane Australia Phone: +61-7-33653732 Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm ** - MD group, RuG - Address: Molecular Dynamics Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Website: http://www.rug.nl/gbb/md __ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox overlap checking
hi roman, On Thu, 2006-03-09 at 17:14 +0100, Roman Holomb wrote: > Dear all, > > I have problem with using genbox > When I try to add more than 20 BF4 molecules in the box (3.2 3.2 3.2) by > > genbox -ci BF4_1.gro -nmol 20 -box 3.2 -o BF4_20.gro probably you need to indicate a bigger van der waals distance by -vdwd for your insert. as an alternative, why don't you stack your molecule with genconf? then each molecule has as much space as in the unit box. regards, daniela > I usualy have connected BF4 molecules. Changes in the vdwradii.dat file > not help. > > Also during adding molecules I can see something like: > > - > "Going to determine what solvent types we have. > There are 0 molecules, 5 charge groups and 5 atoms > There are 0 optimized solvent molecules on node 0 > There are 0 optimized water molecules on node 0 > Grid: 4 x 4 x 4 cells > nri = 7, nrj = 10 > Checking Protein-Solvent overlap: tested 0 pairs, removed 0 atoms. > Checking Solvent-Solvent overlap: tested 0 pairs, removed 0 atoms. > Try 1box_margin = 1.56! > Removed 0 atoms that were outside the box > nri = 7, nrj = 10 > Checking Protein-Solvent overlap: tested 0 pairs, removed 0 atoms. > Checking Solvent-Solvent overlap: tested 0 pairs, removed 0 atoms. > Try 2box_margin = 1.56)! > - > > > So ... overlap testing seem not work but why??? > > Any suggestion? > > Sincerely > Roman > -- Daniela S. Mueller biologist (Diplom, German degree) __ - Molecular Dynamics Group, UQ - Address: School of Molecular and Microbial Sciences (SMMS) Chemistry Building (#68) University of Queensland Qld 4072, Brisbane Australia Phone: +61-7-33653732 Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm ** - MD group, RuG - Address: Molecular Dynamics Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Website: http://www.rug.nl/gbb/md __ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Analysis programs and PBC.
Dear Maxim, On Mon, 2006-02-27 at 18:14 +, Maxim Fedorov wrote: > Dear Daniela, dear all. > Sorry, my previous reply was corrupted > by our server - as a result it lost any sense. > You wrote: > > > > If the molecule you want to analyse is a single molecule, the > > jumping of > > box boundaries does not matter and the analysis tools take that into > > account. But if your molecule is a complex of two or more separate > > subunits, > > What do you exactly mean when you are saying 'subunits' - some separate > molecules or different functional parts of the SAME molecule like > residials in polypeptide/protein chain or sugars in a polysaccharide, etc? > Your answer is of crucial importance for me - now I have only one > molecule (polypeptide) but it contains many residials. As Anton already said, a subunit of a protein is a distinct molecule. The protein I mentioned consisted of two (separate) chains which can jump over the box boundaries independently, so that the complex appears(!!!) to separate (while of course the chains are still interacting across the periodic boundary). If you have one chain, you don't have to worry about jumps. Best regards, Daniela > My best wishes, > > Maxim > > > -- Daniela S. Mueller biologist (Diplom, German degree) __ - Molecular Dynamics Group, UQ - Address: School of Molecular and Microbial Sciences (SMMS) Chemistry Building (#68) University of Queensland Qld 4072, Brisbane Australia Phone: +61-7-33653732 Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm ** - MD group, RuG - Address: Molecular Dynamics Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Website: http://www.rug.nl/gbb/md __ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Analysis programs and PBC.
Hi Maxim, On Mon, 2006-02-27 at 16:56 +, Maxim Fedorov wrote: > Dear Daniela, > > > If the molecule you want to analyse is a single molecule, the > > jumping of > > box boundaries does not matter and the analysis tools take that into > > account. But if your molecule is a complex of two or more separate > > subunits, you might want to remove jumps over the boundaries to > > reassemble the complex again, e.g. to measure the minimum distance to > > the periodic images (and not to the subunit, which should be very > > nearby). > > > > What I actually found with trjconv -pbc nojump was, that two > > conditionsapply if you want to remove jumps: 1) the trajectory has > > to start at the > > initial frame and be continuous; 2) the tpr-file should correspond to > > the initial conformation. If these conditions weren't fulfilled, > > one of > > the subunits was rotated and the complex was reassembled > > incorrectly - > > although the box was rectangular. > > This incorrect rotation seems to be a weird bug, probably the > > referencing to the tpr-structure is a special case-treatment and not > > robust to various setups...? > > Thank you very much for this information. > Could you specify in more details what do you mean when you > Could it be residials of a polypeptide/protein chain or > you mean something else? The protein consists of two chains. During the simulation, one of the chains jumped across the box boundary while the other one stayed on the original side of the box. After using trjconv -pbc nojump on a trajectory fragment starting at a time after the jump, the chain is transformed into the box but with a rotation. It's pretty tricky because you have to be able to recognise this as the wrong assembly, otherwise you would just continue working with a wrong trajectory. I will see if I can submit a bugzilla. daniela > All the best, > > Maxim. > > > > > Success and best regards, > > Daniela > > > -- Daniela S. Mueller biologist (Diplom, German degree) __ - Molecular Dynamics Group, UQ - Address: School of Molecular and Microbial Sciences (SMMS) Chemistry Building (#68) University of Queensland Qld 4072, Brisbane Australia Phone: +61-7-33653732 Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm ** - MD group, RuG - Address: Molecular Dynamics Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Website: http://www.rug.nl/gbb/md __ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Analysis programs and PBC.
Dear Maxim, dear David, On Sun, 2006-02-26 at 22:34 +0100, David van der Spoel wrote: > Maxim Fedorov wrote: > > Dear all, > > > > I have been successfully using Gromacs for a couple years without > > bothering you - > > manual + reading the mailing list was completely enough. > > > > But … this is the second mail for this afternoon. > > > > The question is: are there any analysis programs in GROMACS package > > which are sensitive to Periodic Boundary Conditions or they remove the > > periodicity automatically? > > > > Now I explain in more details what I mean: > > > > Let’s suppose that I have a trajectory file after some MD run with > > PBC. No shuffling, sorting and other things like that – only PBC. > > > > Then I am going to analyze the trajectory with g_rama, g_hbond, g_rdf, > > g_gyrate and, very probably, something else. > > Should I remove the periodicity first or I will be able to analyze the > > trajectory without bothering myself about that issue? > > I have already tried to analyze the PBC runs with and without removal > > of periodicity– the results are the same. > > But may be this is only due to the fact that my molecule didn’t move > > too much during the run and was placed as a whole in the periodic > > cell? And, in a general case I have to remove the periodicity to be > > 100% in the result of analysis. > > > > Sorry, for this, probably, silly question, but I am starting several > > series of simulations - I will be not physically able to check every > > time several hundreds of trajectories with or without periodicity > > removal > > (even with modern scripting languages a human being should take a look > > on the final results, isn't it :-)). > > > > In all programs were it is needed PBC is taken care of. I have recently > built in flags into some of the programs that allow you to control the > removal of periodic boundary conditions (i.e. putting whole molecules in > the box prior to analysis). The reason for this is that we're doing > extensive simulations in vacuo, and putting the molecules back in the > box breaks the analysis. In solvent the default behavior is fine. > > Bottom line is that PBC is treated properly as far as I know. But you > should always check your output :). > If the molecule you want to analyse is a single molecule, the jumping of box boundaries does not matter and the analysis tools take that into account. But if your molecule is a complex of two or more separate subunits, you might want to remove jumps over the boundaries to reassemble the complex again, e.g. to measure the minimum distance to the periodic images (and not to the subunit, which should be very nearby). What I actually found with trjconv -pbc nojump was, that two conditions apply if you want to remove jumps: 1) the trajectory has to start at the initial frame and be continuous; 2) the tpr-file should correspond to the initial conformation. If these conditions weren't fulfilled, one of the subunits was rotated and the complex was reassembled incorrectly - although the box was rectangular. This incorrect rotation seems to be a weird bug, probably the referencing to the tpr-structure is a special case-treatment and not robust to various setups...? Success and best regards, Daniela > > With kindest regards, > > > > Maxim. > > > > Maxim V. Fedorov > > Research Associate. > > -- Daniela S. Mueller biologist (Diplom, German degree) __ - Molecular Dynamics Group, UQ - Address: School of Molecular and Microbial Sciences (SMMS) Chemistry Building (#68) University of Queensland Qld 4072, Brisbane Australia Phone: +61-7-33653732 Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm ** - MD group, RuG - Address: Molecular Dynamics Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Website: http://www.rug.nl/gbb/md __ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
