Re: [gmx-users] interaction lists in idef.h
[EMAIL PROTECTED] wrote: hello all. i am trying to trying to write an analysis program that takes advantage of the gromacs utilities/structures. for my analysis i need to identify each type of interaction in the potential energy function and the atoms involved in each equivalent interaction of the given type. for example, for each different type of bond angle, i would like to identify each triple of bonded atoms forming the given type of bond angle. also i would like to be able to identify each pair of atoms - one of type A and one of type B - that interact through a nonbonded (lennard-jones type) A-B interaction. You can do this by copying how GROMACS does it when it goes to calculated bonded forces... force.c calls calc_bonds() in src/gmxlib/bondfree.c and that calls the functions that were associated with each bonded type in src/gmxlib/ifunc.c i would like to use something like "read_tps_conf" to read a tpr file and then extract these lists of pairs, triples, etc. from the interaction list in the topology data structure. however, after spending some time fiddling around with interaction list data structures such as idef and ilist, it is still not obvious to me how to extract this information. after reading through types/idef.h, it seems that the information i need is stored in these structures, but i still don't understand how they are used. is there a relatively easy way to get these lists of interactions for each interaction type out of the tpr file? and if so, can someone please enlighten me as to how this is done? of course this information can be obtained from the .top file and i have started writing my own utility for extracting this information directly from the .top file. however, if there is a clean way to extract the information from the .tpr file using gromacs utilities that are already written, that would be a big help. Remember that top file atom numbering starts from one, but all the indices in the code are C-style and start from zero. Mark ___ 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] FEP
[EMAIL PROTECTED] wrote: Hi, I would like to perform free energy perturbation using gromacs. I found some tutorial about this type of calculation, but a question is not clear. My calculation is very similar to the calculation described in the tutorial, because I want to change only the non bonded terms. I didn't understand if I need to duplicate also the other terms of the topology file such as bond, angles, pairs, dihedral etc...also when I don't change this type of terms. Thank a lot no, by default the same values will be used. Jacopo ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] interaction lists in idef.h
[EMAIL PROTECTED] wrote: hello all. i am trying to trying to write an analysis program that takes advantage of the gromacs utilities/structures. for my analysis i need to identify each type of interaction in the potential energy function and the atoms involved in each equivalent interaction of the given type. for example, for each different type of bond angle, i would like to identify each triple of bonded atoms forming the given type of bond angle. also i would like to be able to identify each pair of atoms - one of type A and one of type B - that interact through a nonbonded (lennard-jones type) A-B interaction. try checking out similar utilities, like src/tools/mk_angndx.c you may even use that to generate simpler index file as input for your tools. for nonbonded an interaction matrix is stored at the beginning of the idef (idef->ntypes * idef->ntypes entries). i would like to use something like "read_tps_conf" to read a tpr file and then extract these lists of pairs, triples, etc. from the interaction list in the topology data structure. however, after spending some time fiddling around with interaction list data structures such as idef and ilist, it is still not obvious to me how to extract this information. after reading through types/idef.h, it seems that the information i need is stored in these structures, but i still don't understand how they are used. is there a relatively easy way to get these lists of interactions for each interaction type out of the tpr file? and if so, can someone please enlighten me as to how this is done? of course this information can be obtained from the .top file and i have started writing my own utility for extracting this information directly from the .top file. however, if there is a clean way to extract the information from the .tpr file using gromacs utilities that are already written, that would be a big help. thanks to anyone who can help me out here. will noid ___ 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 thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] gromacs mdrun problems
Jonathan Spicer wrote: Hi I'm currently setting up some machines to run gromacs (3.3.1) and have run into a problem with mdrun and mdadm. I have (hopefully) successfully compiled gromacs but when running the demo in /share/tutor/gmxdemo i get either : mdamd: error reading /dev/md-nice : no such file or folder this is part of the OS oftware on your computer for RAID disks. try sourcing the GMXRC file in the gromacs bin dir. or when modifying the demo to include --auto=md or =mdp in the mdrun commands i get mdadm: /dev/md-nice not identified in config file. i know that the mdadm is used in controlling raid devices, however i'm not sure of it's application here or any possible fix for this any help in this in much appreciated many thanks Jonathan Spicer ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] interaction lists in idef.h
hello all. i am trying to trying to write an analysis program that takes advantage of the gromacs utilities/structures. for my analysis i need to identify each type of interaction in the potential energy function and the atoms involved in each equivalent interaction of the given type. for example, for each different type of bond angle, i would like to identify each triple of bonded atoms forming the given type of bond angle. also i would like to be able to identify each pair of atoms - one of type A and one of type B - that interact through a nonbonded (lennard-jones type) A-B interaction. i would like to use something like "read_tps_conf" to read a tpr file and then extract these lists of pairs, triples, etc. from the interaction list in the topology data structure. however, after spending some time fiddling around with interaction list data structures such as idef and ilist, it is still not obvious to me how to extract this information. after reading through types/idef.h, it seems that the information i need is stored in these structures, but i still don't understand how they are used. is there a relatively easy way to get these lists of interactions for each interaction type out of the tpr file? and if so, can someone please enlighten me as to how this is done? of course this information can be obtained from the .top file and i have started writing my own utility for extracting this information directly from the .top file. however, if there is a clean way to extract the information from the .tpr file using gromacs utilities that are already written, that would be a big help. thanks to anyone who can help me out here. will noid ___ 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] biased potential in Gromacs
Dear Argyrios, You may want to check the flooding option. Ran. Argyrios Karatrantos wrote: > Hi everybody, > > i am working in vapor-liquid phase transitions of polyelectrolyte solutions > > is it possible to use a biased potential functon in Gromacs in order to > overcome the free energy barrier between liquid-vapor phases? > > if yes, how this can be implemented in gromacs? > > thanks, in advance all of the people for their help. > > > > > > > Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel > and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 > > ___ > 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 > > -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ 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] gromacs mdrun problems
Hi, On Monday, 3. September 2007 15:44, Jonathan Spicer wrote: > Hi > I'm currently setting up some machines to run gromacs (3.3.1) and > have run into a problem with mdrun and mdadm. I have (hopefully) > successfully compiled gromacs but when running the demo in > /share/tutor/gmxdemo i get either : > > mdamd: error reading /dev/md-nice : no such file or folder > > or when modifying the demo to include --auto=md or =mdp in the mdrun > commands i get > > mdadm: /dev/md-nice not identified in config file. > > i know that the mdadm is used in controlling raid devices, however i'm > not sure of it's application here or any possible fix for this Something is broken or not complete in your gromacs installation, give us some more details of your installation. Try: which mdrun (should be your gromacs path) If it s say something like: not found you can try source GROMACSDIR/bin/GMXRC > > any help in this in much appreciated > many thanks > Jonathan Spicer Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ 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] FEP
Hi, I would like to perform free energy perturbation using gromacs. I found some tutorial about this type of calculation, but a question is not clear. My calculation is very similar to the calculation described in the tutorial, because I want to change only the non bonded terms. I didn't understand if I need to duplicate also the other terms of the topology file such as bond, angles, pairs, dihedral etc...also when I don't change this type of terms. Thank a lot Jacopo ___ 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] biased potential in Gromacs
Hi everybody, i am working in vapor-liquid phase transitions of polyelectrolyte solutions is it possible to use a biased potential functon in Gromacs in order to overcome the free energy barrier between liquid-vapor phases? if yes, how this can be implemented in gromacs? thanks, in advance all of the people for their help. Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ___ 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] gromacs mdrun problems
Hi I'm currently setting up some machines to run gromacs (3.3.1) and have run into a problem with mdrun and mdadm. I have (hopefully) successfully compiled gromacs but when running the demo in /share/tutor/gmxdemo i get either : mdamd: error reading /dev/md-nice : no such file or folder or when modifying the demo to include --auto=md or =mdp in the mdrun commands i get mdadm: /dev/md-nice not identified in config file. i know that the mdadm is used in controlling raid devices, however i'm not sure of it's application here or any possible fix for this any help in this in much appreciated many thanks Jonathan Spicer ___ 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] Energy Minimisation problem
supti mukherjee wrote: Dear all, I was minimising a protein structure. I added polar hydrogens to the protein by some program and then proceeded for the energy minimisation. I chose Conjugate Gradient of 1000 steps with emtol as 100. The mdrun came out with the following error. " During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 17052 ]" Can anybody please help me in identifying my mistake? Try the general procedure outlined here... http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation Mark ___ 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] Energy Minimisation problem
Dear all, I was minimising a protein structure. I added polar hydrogens to the protein by some program and then proceeded for the energy minimisation. I chose Conjugate Gradient of 1000 steps with emtol as 100. The mdrun came out with the following error. " During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 17052 ]" Can anybody please help me in identifying my mistake? Thanks in advance. Yours truly Supti Mukhopadhyay PhD Student, NIMHANS, Bangalore, India. -- ___ 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
