Re: [gmx-users] about the bond connection between different groups
Hi He Yang, Justin, You have said bonds between distinct molecules require a merged topology. Is there any introduction in the manual or Do you have any example about the merged topology? A merged topology contains multiple moleculetype definitions in one topol.top. Discussions are in the archives. Bonds can only be defined within moleculetypes, not between them. So you'll need to combine moleculetypes to create a bond between groups. For this you have to renumber all atoms from one of the moleculetypes, starting at N+1, with N being the number of the last atom of the first moleculetype. You also have to renumber the indices for all other blocks ([bonds], [angles], etc...). Then combine the blocks and finally add the new bond. If it is a proper bond, you should also consider adding the angles and dihedrals involved in the interaction. Note again, merging to create a bond does not mean adding multiple moleculetypes in one topol.top! Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] No such moleculetype Na
Hi, I am performing the simulation of DNA in Gromacs using AMBER03 force field. The charge on the system is large (-23). I get grompp error when I add the relevant number of Na+ atoms. Program grompp_mpi, VERSION 3.3.1 Source code file: toppush.c, line: 1293 Fatal error: No such moleculetype Na But the atom type is present in ffamber03.rtp. I tried changing the atom name to NA and Na+. But I still get similar error. Kindly help. Regards, Swati -- Swati kaushik Research Scholar Prof.Sowdhamini's lab National Centre for Biological Sciences Tata Institute of Fundamental Research GKVK, Bellary Road ,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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] No such moleculetype Na
Hi Swati, Fatal error: No such moleculetype Na But the atom type is present in ffamber03.rtp. I tried changing the atom name to NA and Na+. But I still get similar error. Kindly help. It doesn't complain about the atom type, but about the moleculetype. Did you #include ions.itp? That file contains the moleculetype definitions for a series of ions, including Na/NA/NA+. The naming depends on the force field. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] No such moleculetype Na
Hi Tsjerk, Thanks for your reply. ions.itp is already included in topology file. However after you mentioned I checked the ions.itp file. But I think it defines molecule type only for gromacs force fields and the OPLS force field. The headers are only these three #ifdef _FF_GROMACS #ifdef _FF_GROMOS96 #ifdef _FF_OPLS Is this a problem with my GROMACS installation? Kindly advice. Thanks. Swati Hi Swati, Fatal error: No such moleculetype Na But the atom type is present in ffamber03.rtp. I tried changing the atom name to NA and Na+. But I still get similar error. Kindly help. It doesn't complain about the atom type, but about the moleculetype. Did you #include ions.itp? That file contains the moleculetype definitions for a series of ions, including Na/NA/NA+. The naming depends on the force field. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] -center -fit dodecahedron : dimer
Dear Gromacs Users, I am performing a MD simulation of a dimer in a dodecahedron box. The simulation stopped after 8 ns (power cut) and i had to restart to complete it fully to 12 ns. I then concatenated the two trajectories using trjcat trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center -boxcenter tric -o center.xtc trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc 1. The above procedures does not center the molecule in the box. 2. The box seems to shift from one corner to the center. Especially for the duration 8-12 ns (my restart run) I feel I am missing something here. Kindly advice. regards, nahren ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] No such moleculetype Na
Hi Swati, Sorry, I wasn't paying that much attention indeed and failed to notice you were dealing with Amber. There's nothing wrong with your installation in this regard; Gromacs just does not have Amber included by default. I'm not sure if there's an ions.itp for Amber somewhere, but it's not too hard writing the moleculetype 'Na' yourself. Just take one of the ones in ions.itp and set the names and atom type accordingly. Hope it helps, Tsjerk On Wed, Apr 22, 2009 at 10:14 AM, swa...@ncbs.res.in wrote: Hi Tsjerk, Thanks for your reply. ions.itp is already included in topology file. However after you mentioned I checked the ions.itp file. But I think it defines molecule type only for gromacs force fields and the OPLS force field. The headers are only these three #ifdef _FF_GROMACS #ifdef _FF_GROMOS96 #ifdef _FF_OPLS Is this a problem with my GROMACS installation? Kindly advice. Thanks. Swati Hi Swati, Fatal error: No such moleculetype Na But the atom type is present in ffamber03.rtp. I tried changing the atom name to NA and Na+. But I still get similar error. Kindly help. It doesn't complain about the atom type, but about the moleculetype. Did you #include ions.itp? That file contains the moleculetype definitions for a series of ions, including Na/NA/NA+. The naming depends on the force field. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-us...@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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-us...@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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] -center -fit dodecahedron : dimer
Hi Nahren, trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center -boxcenter tric -o center.xtc trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc 1. The above procedures does not center the molecule in the box. You first center and then do a fit. The fitted trajectory will only be centered if the reference (proem.tpr) is (and then you can skip the second step anyway). 2. The box seems to shift from one corner to the center. Especially for the duration 8-12 ns (my restart run) What do you mean with this? Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] -center -fit dodecahedron : dimer
nahren manuel wrote: Dear Gromacs Users, I am performing a MD simulation of a dimer in a dodecahedron box. The simulation stopped after 8 ns (power cut) and i had to restart to complete it fully to 12 ns. I then concatenated the two trajectories using trjcat trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center -boxcenter tric -o center.xtc trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc 1. The above procedures does not center the molecule in the box. The last operation fits to a structure, permitting rotations and translations. If the target is not centered in its box... 2. The box seems to shift from one corner to the center. Especially for the duration 8-12 ns (my restart run) I feel I am missing something here. Kindly advice. It's a periodic box - a mathematical construction. The simulation doesn't care where the atoms go in relation to it. If you care, you can apply trjconv afterwards. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_cluster output
Hi, I have a query regarding g_cluster output. I gave the command g_cluster -f ../const_temp_20ns_0.pdb -s ../../md_0.tpr -sz -tr -cl -wcl 25 -cutoff 0.2 It is written in the clusters.log file that the middle structures of each cluster is written in the clusters.pdb file. How is this middle structure obtained ? The coordinates of the middle structure do not match with any of the structures in that particular cluster. Is the middle structure same as the average structure. if so what is the criteria to get the middle structure. Any suggestions regarding this will be very helpful. Thanks in advance, Sarbani___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] -center -fit dodecahedron : dimer
Dear Gormacs User, I have now created a new tpr in which the protein is centered. trjconv -f promd.xtc -s tprdodecasolv.tpr -center -boxcenter tric -pbc mol -ur compact -o center.xtc trjconv -s tprdodecasolv.tpr -fit rot+trans -f center.xtc -o fit.xtc I see the dimer getting split in some of the frames of fit.xtc.? 2. The box seems to shift from one corner to the center. Especially for the duration 8-12 ns (my restart run) What do you mean with this? I actually see my dodeca box jumping from one end of the viewer to another ( in VMD as well as in ngmx) thanks for your attention and reply. regards nahren --- On Wed, 4/22/09, Tsjerk Wassenaar tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] -center -fit dodecahedron : dimer To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, April 22, 2009, 2:50 PM Hi Nahren, trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center -boxcenter tric -o center.xtc trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc 1. The above procedures does not center the molecule in the box. You first center and then do a fit. The fitted trajectory will only be centered if the reference (proem.tpr) is (and then you can skip the second step anyway). 2. The box seems to shift from one corner to the center. Especially for the duration 8-12 ns (my restart run) What do you mean with this? Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_cluster output
sarbani chattopadhyay wrote: Hi, I have a query regarding g_cluster output. I gave the command g_cluster -f ../const_temp_20ns_0.pdb -s ../../md_0.tpr -sz -tr -cl -wcl 25 -cutoff 0.2 It is written in the clusters.log file that the middle structures of each cluster is written in the clusters.pdb file. How is this middle structure obtained ? The coordinates of the middle structure do not match with any of the structures in that particular cluster. Is the middle structure same as the average structure. if so what is the criteria to get the middle structure. Start with g_cluster -h. That will tell you what the default clustering algorithm you're using is, which may in turn indicate what the middle of a cluster might mean. Obviously an average structure need not be a member of the set (just as for a set of numbers) and need not be physical either. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] -center -fit dodecahedron : dimer
nahren manuel wrote: Dear Gormacs User, I have now created a new tpr in which the protein is centered. trjconv -f promd.xtc -s tprdodecasolv.tpr -center -boxcenter tric -pbc mol -ur compact -o center.xtc trjconv -s tprdodecasolv.tpr -fit rot+trans -f center.xtc -o fit.xtc I see the dimer getting split in some of the frames of fit.xtc.? You're centering on some group, then allowing translations to fit to a structure that might have some different center. So there's no great suprise that the result need not be centered. Re-think the order of your operations. Mark 2. The box seems to shift from one corner to the center. Especially for the duration 8-12 ns (my restart run) What do you mean with this? I actually see my dodeca box jumping from one end of the viewer to another ( in VMD as well as in ngmx) thanks for your attention and reply. regards nahren --- On *Wed, 4/22/09, Tsjerk Wassenaar /tsje...@gmail.com/* wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] -center -fit dodecahedron : dimer To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, April 22, 2009, 2:50 PM Hi Nahren, trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center -boxcenter tric -o center.xtc trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc 1. The above procedures does not center the molecule in the box. You first center and then do a fit. The fitted trajectory will only be centered if the reference (proem.tpr) is (and then you can skip the second step anyway). 2. The box seems to shift from one corner to the center. Especially for the duration 8-12 ns (my restart run) What do you mean with this? Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org /mc/compose?to=gmx-us...@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 gmx-users-requ...@gromacs.org /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:binding energy
Hi, I am performing MD simulations for peptide(ligand)-receptor complex. I dont know how to calculate the binding energy for the complex and individual structures using gromacs version 4. Can anyone please help me out. Regards, Archana. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] No such moleculetype Na
Hi Tsjerk, Thanks for your suggestion.I tried to change the ions.itp as follows : #ifdef _FF_AMBER03 [ moleculetype ] ; molname nrexcl Na+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 Na 1 Na Na 1 1 #endif But still I am getting same problem.Kindly advice. Regards, Swati Hi Swati, Sorry, I wasn't paying that much attention indeed and failed to notice you were dealing with Amber. There's nothing wrong with your installation in this regard; Gromacs just does not have Amber included by default. I'm not sure if there's an ions.itp for Amber somewhere, but it's not too hard writing the moleculetype 'Na' yourself. Just take one of the ones in ions.itp and set the names and atom type accordingly. Hope it helps, Tsjerk On Wed, Apr 22, 2009 at 10:14 AM, swa...@ncbs.res.in wrote: Hi Tsjerk, Thanks for your reply. ions.itp is already included in topology file. However after you mentioned I checked the ions.itp file. But I think it defines molecule type only for gromacs force fields and the OPLS force field. The headers are only these three #ifdef _FF_GROMACS #ifdef _FF_GROMOS96 #ifdef _FF_OPLS Is this a problem with my GROMACS installation? Kindly advice. Thanks. Swati Hi Swati, Fatal error: No such moleculetype Na But the atom type is present in ffamber03.rtp. I tried changing the atom name to NA and Na+. But I still get similar error. Kindly help. It doesn't complain about the atom type, but about the moleculetype. Did you #include ions.itp? That file contains the moleculetype definitions for a series of ions, including Na/NA/NA+. The naming depends on the force field. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Identical energies generated in a rerun calculation ... but ...
Dear users, I am experiencing some troubles in using GMX 4.0.4 trying to rerun trajectories and obtaining energies for single residues and/or portion of proteins. According to the mdrun command help and to my experience with the previous versions of GROMACS, I have edited my mdp file including the desired groups for energy calculation, grompped it and reruned the previous calculation with the original trr trajectory. I have noticed a different behaviour of mdrun plus -rerun flag between the usage of a single CPU or the original number of CPU used in the production run: that is, in the original production run I have used 24 CPU (12 for PME, nosum flag used), in the trajectory rerun step I have tried to use both 24 CPU or single CPU and the result was different and in the case of parallel run strange. The parallel rerun energy file led to an energy file made of a column of the same number, whereas the single CPU one led to a normal energy trend vs time: interestingly, the first value of this last calculation coincided with the one repeated in the previous strange file. Hence, the single CPU recalculation works correctly, despite the fact that (as expected) it takes longer time for huge trajectories with respect to parallel run: but what's wrong with parallel rerun ? Is it a bug of the newer version of the code or am I missing something in the comprehnsion of how the rerun issue is working at code level ? It seems to be more likely a code bug ... but I wait for your comments and/or suggestions. Thanx in advance Luca ___ Luca Mollica Biomolecular NMR Laboratory 1B4 Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute Via Olgettina 58 20132 Milano Italy mollica.l...@hsr.it; lucamoll...@gmail.com Tel: 0039-022643-3497(Lab)/5622(Uff)/4348(Uff2) 0039-024951(Mobile Ext.Call) Fax: 0039-0226434153 People aren't overcome by situations or outside forces. Defeat comes from within. Banana Yoshimoto (Kitchen) - La tua mano puo' lasciare un segno importante. Dona il tuo 5 per mille al San Raffaele di Milano. E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi Finanziamento della ricerca sanitaria il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Per saperne di piu': 5permi...@hsr.it o vai sul sito http://www.5xmille.org. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Identical energies generated in a rerun calculation ... but ...
Luca Mollica wrote: Dear users, I am experiencing some troubles in using GMX 4.0.4 trying to rerun trajectories and obtaining energies for single residues and/or portion of proteins. According to the mdrun command help and to my experience with the previous versions of GROMACS, I have edited my mdp file including the desired groups for energy calculation, grompped it and reruned the previous calculation with the original trr trajectory. I have noticed a different behaviour of mdrun plus -rerun flag between the usage of a single CPU or the original number of CPU used in the production run: that is, in the original production run I have used 24 CPU (12 for PME, nosum flag used), in the trajectory rerun step I have tried to use both 24 CPU or single CPU and the result was different and in the case of parallel run strange. The parallel rerun energy file led to an energy file made of a column of the same number, whereas the single CPU one led to a normal energy trend vs time: interestingly, the first value of this last calculation coincided with the one repeated in the previous strange file. Hence, the single CPU recalculation works correctly, despite the fact that (as expected) it takes longer time for huge trajectories with respect to parallel run: but what's wrong with parallel rerun ? Is it a bug of the newer version of the code or am I missing something in the comprehnsion of how the rerun issue is working at code level ? It seems to be more likely a code bug ... but I wait for your comments and/or suggestions. Ordinarily I'd suggest you'd probably managed to mismatch trajectory or run input files, but there was another report less than 24 hours ago of what appears to be a single-processor rerun producing the same numbers. This suggests that a single-processor rerun is loading a structure that is the same as the first one loaded by a multi-processor rerun (i.e. the first one in the trajectory) and then not ever loading a new one correctly. Can you see if these values are consistent with those reported for this step for the original simulation? They might differ slightly because of the timing of neighbour-searching. What step numbers are being reported in the rerun .log file? I had a quick look at the code, but couldn't see any problem in do_md(). The first frame gets read with read_first_frame, the data gets copied from rerun_fr to the appropriate places, and at the end of the loop, read_next_frame is called. There doesn't appear to be any way you could get a difference between single- or multi-processor runs in the way you describe. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] No such moleculetype Na
Hi Tsjerk, Thanks for your suggestions.After including molecule types from ions.itp for OPLS force field,its working fine now. Thanks again. Regards, Swati Hi Swati, Sorry, I wasn't paying that much attention indeed and failed to notice you were dealing with Amber. There's nothing wrong with your installation in this regard; Gromacs just does not have Amber included by default. I'm not sure if there's an ions.itp for Amber somewhere, but it's not too hard writing the moleculetype 'Na' yourself. Just take one of the ones in ions.itp and set the names and atom type accordingly. Hope it helps, Tsjerk On Wed, Apr 22, 2009 at 10:14 AM, swa...@ncbs.res.in wrote: Hi Tsjerk, Thanks for your reply. ions.itp is already included in topology file. However after you mentioned I checked the ions.itp file. But I think it defines molecule type only for gromacs force fields and the OPLS force field. The headers are only these three #ifdef _FF_GROMACS #ifdef _FF_GROMOS96 #ifdef _FF_OPLS Is this a problem with my GROMACS installation? Kindly advice. Thanks. Swati Hi Swati, Fatal error: No such moleculetype Na But the atom type is present in ffamber03.rtp. I tried changing the atom name to NA and Na+. But I still get similar error. Kindly help. It doesn't complain about the atom type, but about the moleculetype. Did you #include ions.itp? That file contains the moleculetype definitions for a series of ions, including Na/NA/NA+. The naming depends on the force field. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RMSD of Aminoacids
Hi, I'm trying to compare two proteins with the same number of aminoacids with g_confrms, and it works all right, but it gives me the RMSD of the hole protein, and I need the distances (or deviations) of each aminoacid. I know this data shoul be there, but I don't know how to get it (I've got the mean structure of each protein, calculated with g_rmsf, but this data is not fitted each other) Hopping to be clear. Thanks in advance Andy. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] about the bond connection between different groups
Hi Tsjerk, Thank you for your reply. SO you mean I can just define the bond in one moleculetype.As what you said, I have to renumber all atoms from one of the moleculetypes, starting at N+1, with N being the number of the last atom of the first moleculetype .Then I wonder which molecule type the atom N+1 belongs to . Also, I wonder how to define the new atom N+1's moleculetype in the gro file . I just am not sure about that. Can you give me much more information about that? Thank you very much. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, April 21, 2009 11:22 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] about the bond connection between different groups Hi He Yang, Justin, You have said bonds between distinct molecules require a merged topology. Is there any introduction in the manual or Do you have any example about the merged topology? A merged topology contains multiple moleculetype definitions in one topol.top. Discussions are in the archives. Bonds can only be defined within moleculetypes, not between them. So you'll need to combine moleculetypes to create a bond between groups. For this you have to renumber all atoms from one of the moleculetypes, starting at N+1, with N being the number of the last atom of the first moleculetype. You also have to renumber the indices for all other blocks ([bonds], [angles], etc...). Then combine the blocks and finally add the new bond. If it is a proper bond, you should also consider adding the angles and dihedrals involved in the interaction. Note again, merging to create a bond does not mean adding multiple moleculetypes in one topol.top! Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about the bond connection between different groups
You have: [ moleculetype ] A [atoms] 1 ... N and [ moleculetype ] B [atoms] 1 ... M and want to make a bond between atom X of A and Y of B. So you have to merge A and B into: [ moleculetype ] A+B [atoms] 1 ... N N+1 ... N+M with a.o.: [bonds] X Y+N type bond-parameters. I hope this is clear enough. If it isn't, read Chapter 5 of the manual thoroughly. Cheers, Tsjerk On Wed, Apr 22, 2009 at 5:30 PM, He, Yang yang...@mavs.uta.edu wrote: Hi Tsjerk, Thank you for your reply. SO you mean I can just define the bond in one moleculetype.As what you said, I have to renumber all atoms from one of the moleculetypes, starting at N+1, with N being the number of the last atom of the first moleculetype .Then I wonder which molecule type the atom N+1 belongs to . Also, I wonder how to define the new atom N+1's moleculetype in the gro file . I just am not sure about that. Can you give me much more information about that? Thank you very much. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, April 21, 2009 11:22 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] about the bond connection between different groups Hi He Yang, Justin, You have said bonds between distinct molecules require a merged topology. Is there any introduction in the manual or Do you have any example about the merged topology? A merged topology contains multiple moleculetype definitions in one topol.top. Discussions are in the archives. Bonds can only be defined within moleculetypes, not between them. So you'll need to combine moleculetypes to create a bond between groups. For this you have to renumber all atoms from one of the moleculetypes, starting at N+1, with N being the number of the last atom of the first moleculetype. You also have to renumber the indices for all other blocks ([bonds], [angles], etc...). Then combine the blocks and finally add the new bond. If it is a proper bond, you should also consider adding the angles and dihedrals involved in the interaction. Note again, merging to create a bond does not mean adding multiple moleculetypes in one topol.top! Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-us...@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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-us...@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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] about the bond connection between different groups
Hi Tsjerk, Thank you very much for your introduction about how to merge two moleculetypes. I just follow your instructions as listed below; I have two moleculetypes named DNA and ICE. This is what I include in topology file: #include dna.itp #include ICE.itp [ moleculetype ] ; molnamecylind DNA+ICE 1 [ atoms ] ; nr type resnr res atom cgnrcharge mass 1bA 1 DNAbA 1 0 178.0 ... 20lA 1 ICElA20 0 134.0 [ angles ] ... [ dihedrals ] ... [ system ] ; Name CGMD [ molecules ] ; Compound #mols DNA+ICE 1 I have 19 atoms in DNA and only one atom in ICE. Also, I have consider adding the angles and dihedrals involved in the interaction. Then, I also include individual itp file for the DNA and ICE ,respectively . In addition , I want to freeze the atom in ICE and that is what I include in .mdp file : energygrp_excl = ICE ICE ; Non-equilibrium MD ; freezegrps =ICE freezedim = Y Y Y [ system ] ; Name CGMD [ molecules ] ; Compound #mols DNA+ICE 1 But when I run this, it shows that: Group ICE not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Can you tell me what is the problem? Thank you for your suggestions. Regards, Yang ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Wednesday, April 22, 2009 11:53 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] about the bond connection between different groups You have: [ moleculetype ] A [atoms] 1 ... N and [ moleculetype ] B [atoms] 1 ... M and want to make a bond between atom X of A and Y of B. So you have to merge A and B into: [ moleculetype ] A+B [atoms] 1 ... N N+1 ... N+M with a.o.: [bonds] X Y+N type bond-parameters. I hope this is clear enough. If it isn't, read Chapter 5 of the manual thoroughly. Cheers, Tsjerk On Wed, Apr 22, 2009 at 5:30 PM, He, Yang yang...@mavs.uta.edu wrote: Hi Tsjerk, Thank you for your reply. SO you mean I can just define the bond in one moleculetype.As what you said, I have to renumber all atoms from one of the moleculetypes, starting at N+1, with N being the number of the last atom of the first moleculetype .Then I wonder which molecule type the atom N+1 belongs to . Also, I wonder how to define the new atom N+1's moleculetype in the gro file . I just am not sure about that. Can you give me much more information about that? Thank you very much. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, April 21, 2009 11:22 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] about the bond connection between different groups Hi He Yang, Justin, You have said bonds between distinct molecules require a merged topology. Is there any introduction in the manual or Do you have any example about the merged topology? A merged topology contains multiple moleculetype definitions in one topol.top. Discussions are in the archives. Bonds can only be defined within moleculetypes, not between them. So you'll need to combine moleculetypes to create a bond between groups. For this you have to renumber all atoms from one of the moleculetypes, starting at N+1, with N being the number of the last atom of the first moleculetype. You also have to renumber the indices for all other blocks ([bonds], [angles], etc...). Then combine the blocks and finally add the new bond. If it is a proper bond, you should also consider adding the angles and dihedrals involved in the interaction. Note again, merging to create a bond does not mean adding multiple moleculetypes in one topol.top! Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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
[gmx-users] np command with GROMACS 4.0.4
Hi! I am trying to do my position restrained dynamic simulation on GROMACS 4.0.4, and I want to use 4 nodes on the cpu cluster available at my campus; I typed in the following grompp command: grompp -np 4 -f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx -maxwarn 10 and it gave me the response that -np is an invalid command. How do I get grompp to rec. that I want to use 4 processors? Because my job script where I have specified 4 nodes, will not work unless I have np 4 included in my grompp. I did see that it works with GROMACS 3.3.3...but is there a way to do it with 4.0.4? Thanks so much! Halie Shah University of Houston, TX U.S. Briggs Lab ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] np command with GROMACS 4.0.4
Halie Shah wrote: Hi! I am trying to do my position restrained dynamic simulation on GROMACS 4.0.4, and I want to use 4 nodes on the cpu cluster available at my campus; I typed in the following grompp command: grompp -np 4 -f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx -maxwarn 10 and it gave me the response that -np is an invalid command. Just obey the almighty grompp and don't bother it with trivialities as the number of processors. Such futilities have been transferred to the able mdrun program. How do I get grompp to rec. that I want to use 4 processors? Because my job script where I have specified 4 nodes, will not work unless I have np 4 included in my grompp. I did see that it works with GROMACS 3.3.3...but is there a way to do it with 4.0.4? Thanks so much! Halie Shah University of Houston, TX U.S. Briggs Lab ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] np command with GROMACS 4.0.4
Halie Shah wrote: Hi! I am trying to do my position restrained dynamic simulation on GROMACS 4.0.4, and I want to use 4 nodes on the cpu cluster available at my campus; I typed in the following grompp command: grompp -np 4 -f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx -maxwarn 10 and it gave me the response that -np is an invalid command. How do I get grompp to rec. that I want to use 4 processors? Because my job script where I have specified 4 nodes, will not work unless I have np 4 included in my grompp. I did see that it works with GROMACS 3.3.3...but is there a way to do it with 4.0.4? The option is unnecessary as of version 4.0; the .tpr file produced can be run on any amount of nodes. -Justin Thanks so much! Halie Shah University of Houston, TX U.S. Briggs Lab ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] np command with GROMACS 4.0.4
You don't need to use -np 4 option to do preprocessing on version 4.0.4. Just do preprocessing without it and use it when you start your simulation like followings: grompp mpirun -np 4 mdrun (if you use MPI for parallel running) kyungchan From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Halie Shah Sent: Wednesday, April 22, 2009 4:01 PM To: gmx-users@gromacs.org Subject: [gmx-users] np command with GROMACS 4.0.4 Hi! I am trying to do my position restrained dynamic simulation on GROMACS 4.0.4, and I want to use 4 nodes on the cpu cluster available at my campus; I typed in the following grompp command: grompp -np 4 -f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx -maxwarn 10 and it gave me the response that -np is an invalid command. How do I get grompp to rec. that I want to use 4 processors? Because my job script where I have specified 4 nodes, will not work unless I have np 4 included in my grompp. I did see that it works with GROMACS 3.3.3...but is there a way to do it with 4.0.4? Thanks so much! Halie Shah University of Houston, TX U.S. Briggs Lab ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about the bond connection between different groups
Dear Yang, It appears that you will either need to either A) create a new index file using the make_ndx utility, or B) modify your existing index file. If you haven't done this procedure before, the first option may be the easiest. A good description of make_ndx is contained in the manual as well as some introductory tutorials. -Steve He, Yang wrote: Hi Tsjerk, Thank you very much for your introduction about how to merge two moleculetypes. I just follow your instructions as listed below; I have two moleculetypes named DNA and ICE. This is what I include in topology file: #include dna.itp #include ICE.itp [ moleculetype ] ; molnamecylind DNA+ICE 1 [ atoms ] ; nr type resnr res atom cgnrcharge mass 1bA 1 DNAbA 1 0 178.0 ... 20lA 1 ICElA20 0 134.0 [ angles ] ... [ dihedrals ] ... [ system ] ; Name CGMD [ molecules ] ; Compound #mols DNA+ICE 1 I have 19 atoms in DNA and only one atom in ICE. Also, I have consider adding the angles and dihedrals involved in the interaction. Then, I also include individual itp file for the DNA and ICE ,respectively . In addition , I want to freeze the atom in ICE and that is what I include in .mdp file : energygrp_excl = ICE ICE ; Non-equilibrium MD ; freezegrps =ICE freezedim = Y Y Y [ system ] ; Name CGMD [ molecules ] ; Compound #mols DNA+ICE 1 But when I run this, it shows that: Group ICE not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Can you tell me what is the problem? Thank you for your suggestions. Regards, Yang ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Wednesday, April 22, 2009 11:53 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] about the bond connection between different groups You have: [ moleculetype ] A [atoms] 1 ... N and [ moleculetype ] B [atoms] 1 ... M and want to make a bond between atom X of A and Y of B. So you have to merge A and B into: [ moleculetype ] A+B [atoms] 1 ... N N+1 ... N+M with a.o.: [bonds] X Y+N type bond-parameters. I hope this is clear enough. If it isn't, read Chapter 5 of the manual thoroughly. Cheers, Tsjerk On Wed, Apr 22, 2009 at 5:30 PM, He, Yang yang...@mavs.uta.edu wrote: Hi Tsjerk, Thank you for your reply. SO you mean I can just define the bond in one moleculetype.As what you said, I have to renumber all atoms from one of the moleculetypes, starting at N+1, with N being the number of the last atom of the first moleculetype .Then I wonder which molecule type the atom N+1 belongs to . Also, I wonder how to define the new atom N+1's moleculetype in the gro file . I just am not sure about that. Can you give me much more information about that? Thank you very much. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, April 21, 2009 11:22 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] about the bond connection between different groups Hi He Yang, Justin, You have said bonds between distinct molecules require a merged topology. Is there any introduction in the manual or Do you have any example about the merged topology? A merged topology contains multiple moleculetype definitions in one topol.top. Discussions are in the archives. Bonds can only be defined within moleculetypes, not between them. So you'll need to combine moleculetypes to create a bond between groups. For this you have to renumber all atoms from one of the moleculetypes, starting at N+1, with N being the number of the last atom of the first moleculetype. You also have to renumber the indices for all other blocks ([bonds], [angles], etc...). Then combine the blocks and finally add the new bond. If it is a proper bond, you should also consider adding the angles and dihedrals involved in the interaction. Note again, merging to create a bond does not mean adding multiple moleculetypes in one topol.top! Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about the bond connection between different groups
He, Yang wrote: Hi Tsjerk, Thank you very much for your introduction about how to merge two moleculetypes. I just follow your instructions as listed below; I have two moleculetypes named DNA and ICE. This is what I include in topology file: #include dna.itp #include ICE.itp Depending on the contents of these two molecules, they may not be necessary. The merged topology, in theory, is a combination of these two moleculetype definitions. [ moleculetype ] ; molnamecylind DNA+ICE 1 [ atoms ] ; nr type resnr res atom cgnrcharge mass 1bA 1 DNAbA 1 0 178.0 ... 20lA 1 ICElA20 0 134.0 [ angles ] ... [ dihedrals ] ... [ system ] ; Name CGMD [ molecules ] ; Compound #mols DNA+ICE 1 I have 19 atoms in DNA and only one atom in ICE. Also, I have consider adding the angles and dihedrals involved in the interaction. Then, I also include individual itp file for the DNA and ICE ,respectively . In addition , I want to freeze the atom in ICE and that is what I include in .mdp file : energygrp_excl = ICE ICE ; Non-equilibrium MD ; freezegrps =ICE freezedim = Y Y Y [ system ] ; Name CGMD [ molecules ] ; Compound #mols DNA+ICE 1 But when I run this, it shows that: Group ICE not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Can you tell me what is the problem? Thank you for your suggestions. You have defined a molecule called DNA+ICE so you need to use an index group to decompose its components into those that you wish to use. -Justin Regards, Yang ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Wednesday, April 22, 2009 11:53 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] about the bond connection between different groups You have: [ moleculetype ] A [atoms] 1 ... N and [ moleculetype ] B [atoms] 1 ... M and want to make a bond between atom X of A and Y of B. So you have to merge A and B into: [ moleculetype ] A+B [atoms] 1 ... N N+1 ... N+M with a.o.: [bonds] X Y+N type bond-parameters. I hope this is clear enough. If it isn't, read Chapter 5 of the manual thoroughly. Cheers, Tsjerk On Wed, Apr 22, 2009 at 5:30 PM, He, Yang yang...@mavs.uta.edu wrote: Hi Tsjerk, Thank you for your reply. SO you mean I can just define the bond in one moleculetype.As what you said, I have to renumber all atoms from one of the moleculetypes, starting at N+1, with N being the number of the last atom of the first moleculetype .Then I wonder which molecule type the atom N+1 belongs to . Also, I wonder how to define the new atom N+1's moleculetype in the gro file . I just am not sure about that. Can you give me much more information about that? Thank you very much. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, April 21, 2009 11:22 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] about the bond connection between different groups Hi He Yang, Justin, You have said bonds between distinct molecules require a merged topology. Is there any introduction in the manual or Do you have any example about the merged topology? A merged topology contains multiple moleculetype definitions in one topol.top. Discussions are in the archives. Bonds can only be defined within moleculetypes, not between them. So you'll need to combine moleculetypes to create a bond between groups. For this you have to renumber all atoms from one of the moleculetypes, starting at N+1, with N being the number of the last atom of the first moleculetype. You also have to renumber the indices for all other blocks ([bonds], [angles], etc...). Then combine the blocks and finally add the new bond. If it is a proper bond, you should also consider adding the angles and dihedrals involved in the interaction. Note again, merging to create a bond does not mean adding multiple moleculetypes in one topol.top! Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-users@gromacs.org
Re: [gmx-users] RMSD of Aminoacids
Andy Torres wrote: Hi, I'm trying to compare two proteins with the same number of aminoacids with g_confrms, and it works all right, but it gives me the RMSD of the hole protein, and I need the distances (or deviations) of each aminoacid. I know this data shoul be there, but I don't know how to get it (I've got the mean structure of each protein, calculated with g_rmsf, but this data is not fitted each other) Have a look at g_confrms -h. Probably with the right index groups constructed you can fit with one group and observe the RMSD with another. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem in topology file of protein-lipid bilayer system for grompp
Dear Justin I am doing simulation of membrane protein .I follow your tutorial for that I think its perfect for that. But I am getting problem in doing inflategro step, I alredy discuss this problem with you but now I am starting everything fresh I have completed upto concatanation of protein with lipid bilayer after that for packing of lipid around protein I am using inflategro script from teleman website . Problem came in second step of inflategro i.e for energy minimisation for this I need topology file of protein-lipid system. I am giving you information in detail i.e - for topology file I have made changes in topol.top file which I got from pdb2gmx command in first step for protein processing ,the topol .top file is like this- File 'topol.top' was generated ; By user: nitu (504) ; On host: localhost.localdomain ; At date: Thu Apr 16 23:20:48 2009 ; ; This is your topology file ; Grunge ROck MAChoS ; ; Include forcefield parameters #include ffG53a6.itp ; Include chain topologies #include topol_A.itp #include topol_B.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Grunge ROck MAChoS [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 ** And the change topology file is like this- ; Include forcefield parameters #include ffG53a6_lipid.itp ; Include chain topologies #include topol_A.itp #include topol_B.itp #ifdef POSRES #include posre_A.itp #include posre_B.itp #endif ; Include DMPC chain topology #include dmpc.itp [ system ] ; Name Protein in DMPC bilayer [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 DMPC 128 but when I gave this topology file to grompp it shws error- no. of coordinates in coordinate file doesn,t mach the topology file . Can you suggest me something for making topology file for protein-lipid bilayer system. Is there any other method for making topology file ,I have read in mannual chapter 5 but there is also mentioned same method. If possible please help me becoz without solving this problem I can't move for furthur processing . * My gro file of protein shows 9902 atoms . As you ask in previous mail is .itp file have [ molecules ] section the answer is the .itp file haven't molecules section it have [molecule type ] section can it also create problem for topology file working. Thanks a lot justin . I am waiting for your reply. Nitu sharma School of life sciences Jawaherlal Nehru University New delhi , 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
