Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem
albita...@virgilio.it wrote: Hi, I came back to my original stretching potential in tabulated form and I have still problems... when running a geometry optimization the results are like that: **+ ^MStep 635, Epot=2.259501e+02, Fnorm=4.086e+00, Fmax=1.886e+01 (atom 34) ^MStep 636, Epot=2.259499e+02, Fnorm=3.847e+00, Fmax=1.992e+01 (atom 33) ^MStep 637, Epot=2.259495e+02, Fnorm=1.002e+01, Fmax=5.408e+01 (atom 33) ^MStep 638, Epot=2.259449e+02, Fnorm=1.026e+01, Fmax=4.098e+01 (atom 34) ^MStep 639, Epot=2.259393e+02, Fnorm=2.193e+01, Fmax=1.159e+02 (atom 35) ^MStep 640, Epot=2.259364e+02, Fnorm=1.469e+01, Fmax=7.064e+01 (atom 34) ^MStep 641, Epot=2.259335e+02, Fnorm=1.281e+01, Fmax=7.154e+01 (atom 34) ^MStep 642, Epot=2.259315e+02, Fnorm=5.803e+00, Fmax=2.861e+01 (atom 35) ^MStep 643, Epot=2.259314e+02, Fnorm=6.332e+00, Fmax=3.116e+01 (atom 34) ^MStep 644, Epot=2.259310e+02, Fnorm=3.550e+00, Fmax=1.502e+01 (atom 34) Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 0.1 as if the system is frozen. My system here is an isolated, linear and finite-length chain. When running an md simulation I got the error: --- Program mdrun_mpi, VERSION 4.0.5 Source code file: bondfree.c, line: 1772 Fatal error: A tabulated bond interaction table number 0 is out of the table range: r 1.815411, between table indices 1815 and 1816, table length 1001 --- The tabulated potential is uniformly spaced, the bond type is 8 to exclude LJ interaction between bonded atoms, nrexcl=1 to include 1-3 interactions (as required by MARTINI force field). That seems like it should work. The same system does not have any problem when running simulation with an harmonic stretching potential in both numerical and analytical form. Does anyone have any suggestion for possible solutions or error in the input? Running gmxcheck between various .tpr files may be instructive, e.g. one file may have many more nonbonded interactions, or such. Otherwise, posting your .mdp file and the start of your .top may help us spot a problem. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Custom Force Field
Honman Yau wrote: 2009/10/6 Justin A. Lemkul mailto:jalem...@vt.edu>> Hi again! Thank you very much for the swift reply! If you want to use pdb2gmx, you will need to create all the standard files (.rtp, .hdb, nb.itp, bon.itp, etc), create an entry in FF.dat, and increment the counter at the top of FF.dat. Ah, I'm actually already in the process of writing a script to do that convert my force field files. :) Regarding this though (which I just realised that I should also have asked earlier) - since I am not actually doing any protein simulations or anything that has amino acids in it, do I still need the the /.rtp/, /.hdb/, /.ddb/ files for /pdb2mgx/ to work correctly? These files may not all be necessary (particular .ddb, -n.tdb, and -c.tdb), but .rtp, .hdb, nb.itp, bon.itp, etc. are not protein-specific. They define residues and parameters within a given force field. I did try to increment the counter at the top of /FF.dat/ before I sent the last e-mail but it didn't seem to work (or is that because I was missing files?). If you haven't created the corresponding force field files, you can certainly expect that magic won't work :) Otherwise, it is relatively simple to write your own topology for a limited number of species as .itp files. See Chapter 5 of the manual for the format and requirements of all of these files. I have considered that option and read the manual already. :) It seems to be easier (for someone else who will be picking up where I will have left off) that I get the script running and have /pdb2gmx/ do the job. I suppose it's a matter of choice. It's just about the same amount of work either way, really. Any future users would simply have to #include the .itp files you come up with, and never have to worry even about using pdb2gmx! -Justin Once again, thank you very much and, again, thank you very much in advance! Kind regards Honman -- 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://lists.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] grompp: no such moleculetype
Francesco Pietra wrote: Look at the .mdp file. You will find Non-Protein somewhere. The .mdp I used is not from a tutorial; it is the general purpose - or standard - mdp provided by Martini. It doe not contain the word "protein" The "protein-in-vacuum.mdp from the ubiquitin CG tutoria does contain both "Protein" and "Non-Protein" words. deleting "Non-Protein", the error from running grompp is: Fatal error: Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values This comes up because you've defined one group now for T-coupling and assigned coupling constants and temperatures for two. Haphazard changes to .mdp files will certainly generate these errors. Deleting until the problem goes away never works - it only creates more problems :) Please see the manual for proper use of tc-grps, etc. I'll settle the matter until I can generate ideas, or be less tired to check again for the presence of that mysterious non-protein. The real protein contains chloride ion ligands. I have cleared from them before starting with CG and anyway no trace of cl CL Cl. So that has nothing to do with it. Hope to be able to come again here with a solution of this affair. The best advice - don't blindly use some .mdp file you find because it works for a tutorial. Read it, read the manual, and make changes based on what you actually have in your system. I fully agree. Using "protein-in-vacuum.mdp", although attractive because of "vacuum", was a bold adventure. But the standard mdp I used before is declared to be standard, and my protein is standard. As I said, I'll work hard to come out but before I'll take a few days wandering with my Brittany on the Alps. The Tetraonidae will refresh my mind. What is "standard" for one user is not necessarily "standard" for another. You must almost always make changes to suit your particular system, as a general rule. Thanks for all you did for me (for us) You're welcome. Hopefully everything works out. -Justin francesco -Justin thanks francesco PS: the protein CG file contains TER lines separating the subunits, but the CG .gro file has no TER. -Justin ; ; mod21 | MARTINI 2.1 ; ; Include force field poarameters containing all particle definitions, ; the interaction matrix, plus the topology for water. #include "martini_v2.1.itp" ; Then include the file(s) containing the topologies of other ; molecules present in your system. ; #include "martini_v2.0_lipids.itp" ; #include "martini_v2.0_salt.itp" #include "mod21.itp" ; Define a name for your system [ system ] mod21 ; Define the composition of your system ; The molecule names should correspond to those defined in the itp file(s). [ molecules ] Protein 1 ; DPPC 128 ; W 2000 ; NA+ 20 ; CL- 20 It seems that commenting out ";" is placed correctly. I am sincerely sorry to bother you again. francesco With command $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -n -o mod21.cg.tpr NOTE: System has non-zero total charge: -5.00e+01 processing coordinates... Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCQd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCP1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BSP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SSAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCC3 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCN0 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHN0 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHNd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHNd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSP1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC3) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC4) (more than 20 non-matching atom names) WARNING 2 [file "mod21.cg.top", line 28]: 2875 non-matching atom names atom names from mod21.cg.top will be used atom names from mod21.cg.box.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... conv
Re: [gmx-users] grompp: no such moleculetype
On Mon, Oct 5, 2009 at 8:20 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: > >> I have now used protein-in-vacuum.mdp from the ubiquitin cg tutorial. > > Which tutorial is that? Can you provide a link? http://md.chem.rug.nl/~marrink/coarsegrain.html > >> Again grompp complains that "Fatal error: >> Group Non-Protein 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." (no more complaining about DPPC, now >> more generic non-protein, which increases the confusion) >> >> Having ruled out the .mdp file as responsible for that, it was easy to >> check that both the protein.gro and the protein.itp files only specify >> standard amino acids. >> > > Why have you ruled the .mdp file out? You will probably find the word > "Non-Protein" somewhere in the .mdp file, most likely in T-coupling groups. > If you have a protein in vacuo, the only groups allowed for T-coupling > would be Protein or System, unless you have specifically made some custom > index groups (but you probably don't want to in this case). > > Look at the .mdp file. You will find Non-Protein somewhere. The .mdp I used is not from a tutorial; it is the general purpose - or standard - mdp provided by Martini. It doe not contain the word "protein" The "protein-in-vacuum.mdp from the ubiquitin CG tutoria does contain both "Protein" and "Non-Protein" words. deleting "Non-Protein", the error from running grompp is: Fatal error: Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values > >> I'll settle the matter until I can generate ideas, or be less tired to >> check again for the presence of that mysterious non-protein. The real >> protein contains chloride ion ligands. I have cleared from them before >> starting with CG and anyway no trace of cl CL Cl. >> > > So that has nothing to do with it. > >> Hope to be able to come again here with a solution of this affair. >> > > The best advice - don't blindly use some .mdp file you find because it works > for a tutorial. Read it, read the manual, and make changes based on what > you actually have in your system. I fully agree. Using "protein-in-vacuum.mdp", although attractive because of "vacuum", was a bold adventure. But the standard mdp I used before is declared to be standard, and my protein is standard. As I said, I'll work hard to come out but before I'll take a few days wandering with my Brittany on the Alps. The Tetraonidae will refresh my mind. Thanks for all you did for me (for us) francesco > > -Justin > >> thanks >> francesco >> PS: the protein CG file contains TER lines separating the subunits, >> but the CG .gro file has no TER. >> >> >>> -Justin >>> ; ; mod21 | MARTINI 2.1 ; ; Include force field poarameters containing all particle definitions, ; the interaction matrix, plus the topology for water. #include "martini_v2.1.itp" ; Then include the file(s) containing the topologies of other ; molecules present in your system. ; #include "martini_v2.0_lipids.itp" ; #include "martini_v2.0_salt.itp" #include "mod21.itp" ; Define a name for your system [ system ] mod21 ; Define the composition of your system ; The molecule names should correspond to those defined in the itp file(s). [ molecules ] Protein 1 ; DPPC 128 ; W 2000 ; NA+ 20 ; CL- 20 It seems that commenting out ";" is placed correctly. I am sincerely sorry to bother you again. francesco >> With command >> >> $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -n >> -o mod21.cg.tpr >> >> NOTE: >> System has non-zero total charge: -5.00e+01 >> >> processing coordinates... >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (BCQd - BN0) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SCAC1 - SC1) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (BCP5 - BN0) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SCP1 - SC1) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (BSP5 - BN0) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SSAC1 - SC1) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (BCP5 - BN0) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SCC3 - SC1) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SCQd - SC2) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (BCP5 - BN0) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SCN0 - SC1) >> Warning: atom names in mod
Re: [gmx-users] Custom Force Field
2009/10/6 Justin A. Lemkul Hi again! Thank you very much for the swift reply! > If you want to use pdb2gmx, you will need to create all the standard files > (.rtp, .hdb, nb.itp, bon.itp, etc), create an entry in FF.dat, and increment > the counter at the top of FF.dat. > Ah, I'm actually already in the process of writing a script to do that convert my force field files. :) Regarding this though (which I just realised that I should also have asked earlier) - since I am not actually doing any protein simulations or anything that has amino acids in it, do I still need the the *.rtp*, *.hdb*, *.ddb* files for *pdb2mgx* to work correctly? I did try to increment the counter at the top of *FF.dat* before I sent the last e-mail but it didn't seem to work (or is that because I was missing files?). > Otherwise, it is relatively simple to write your own topology for a limited > number of species as .itp files. See Chapter 5 of the manual for the format > and requirements of all of these files. > I have considered that option and read the manual already. :) It seems to be easier (for someone else who will be picking up where I will have left off) that I get the script running and have *pdb2gmx* do the job. Once again, thank you very much and, again, thank you very much in advance! Kind regards Honman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Custom Force Field
Honman Yau wrote: Dear All, Hello! I spent the last couple of hours reading the GROMACS manual and trying to get my head around the files. One of the things that I want to do is to use a custom force field for ionic liquids related simulations but I don't seem to be able to find instructions on how to do that (probably very trivial...), is there a way to incorporate that into the pdb2gmx interactive force field selection or can you actually specify the force field that you want to use in the command line? Any help would be much appreciated and thank you very much in advance! If you want to use pdb2gmx, you will need to create all the standard files (.rtp, .hdb, nb.itp, bon.itp, etc), create an entry in FF.dat, and increment the counter at the top of FF.dat. Otherwise, it is relatively simple to write your own topology for a limited number of species as .itp files. See Chapter 5 of the manual for the format and requirements of all of these files. -Justin Kind regards, Honman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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://lists.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] grompp: no such moleculetype
Francesco Pietra wrote: I have now used protein-in-vacuum.mdp from the ubiquitin cg tutorial. Which tutorial is that? Can you provide a link? Again grompp complains that "Fatal error: Group Non-Protein 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." (no more complaining about DPPC, now more generic non-protein, which increases the confusion) Having ruled out the .mdp file as responsible for that, it was easy to check that both the protein.gro and the protein.itp files only specify standard amino acids. Why have you ruled the .mdp file out? You will probably find the word "Non-Protein" somewhere in the .mdp file, most likely in T-coupling groups. If you have a protein in vacuo, the only groups allowed for T-coupling would be Protein or System, unless you have specifically made some custom index groups (but you probably don't want to in this case). Look at the .mdp file. You will find Non-Protein somewhere. I'll settle the matter until I can generate ideas, or be less tired to check again for the presence of that mysterious non-protein. The real protein contains chloride ion ligands. I have cleared from them before starting with CG and anyway no trace of cl CL Cl. So that has nothing to do with it. Hope to be able to come again here with a solution of this affair. The best advice - don't blindly use some .mdp file you find because it works for a tutorial. Read it, read the manual, and make changes based on what you actually have in your system. -Justin thanks francesco PS: the protein CG file contains TER lines separating the subunits, but the CG .gro file has no TER. -Justin ; ; mod21 | MARTINI 2.1 ; ; Include force field poarameters containing all particle definitions, ; the interaction matrix, plus the topology for water. #include "martini_v2.1.itp" ; Then include the file(s) containing the topologies of other ; molecules present in your system. ; #include "martini_v2.0_lipids.itp" ; #include "martini_v2.0_salt.itp" #include "mod21.itp" ; Define a name for your system [ system ] mod21 ; Define the composition of your system ; The molecule names should correspond to those defined in the itp file(s). [ molecules ] Protein 1 ; DPPC 128 ; W 2000 ; NA+ 20 ; CL- 20 It seems that commenting out ";" is placed correctly. I am sincerely sorry to bother you again. francesco With command $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -n -o mod21.cg.tpr NOTE: System has non-zero total charge: -5.00e+01 processing coordinates... Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCQd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCP1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BSP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SSAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCC3 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCN0 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHN0 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHNd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHNd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSP1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC3) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC4) (more than 20 non-matching atom names) WARNING 2 [file "mod21.cg.top", line 28]: 2875 non-matching atom names atom names from mod21.cg.top will be used atom names from mod21.cg.box.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 2724 # G96ANGLES: 2860 # PDIHS: 328 # IDIHS: 187 # CONSTR: 745 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/gmxlib/futil.c, line: 345 File input/output error: in
Re: [gmx-users] grompp: no such moleculetype
On Mon, Oct 5, 2009 at 7:31 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> On Mon, Oct 5, 2009 at 4:39 PM, Justin A. Lemkul wrote: >>> >>> Francesco Pietra wrote: Thanks, and beg pardon for the pedestrian mistake. However, I am not yet out. .tpr not generated With command $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -o mod21.cg.tpr There are: 0 OTHER residues There are: 1270 PROTEIN residues There are: 0 DNA residues Analysing Protein... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/readir.c, line: 798 Fatal error: Group DPPC not found in indexfile. Maybe you have non-default groups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. As I said before, I am using the mdp file as provided by MARTINI. >>> Then you haven't yet appropriately #included the .itp file for DPPC. >> >> As I said, I don't understand why about DPPC. The protein is pure >> standard amino acids and nothing else. I am trying to get the files >> for simulation in vacuum. I have reexamined all the stuff and I don't >> see any allusion to a bilayer, unless that comes from the .mdp file. >> The .top I used in these last attempts reads: > > I would suggest looking at the .mdp file; grompp wouldn't be complaining if > there wasn't some input file specifying an unknown molecule. I have now used protein-in-vacuum.mdp from the ubiquitin cg tutorial. Again grompp complains that "Fatal error: Group Non-Protein 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." (no more complaining about DPPC, now more generic non-protein, which increases the confusion) Having ruled out the .mdp file as responsible for that, it was easy to check that both the protein.gro and the protein.itp files only specify standard amino acids. I'll settle the matter until I can generate ideas, or be less tired to check again for the presence of that mysterious non-protein. The real protein contains chloride ion ligands. I have cleared from them before starting with CG and anyway no trace of cl CL Cl. Hope to be able to come again here with a solution of this affair. thanks francesco PS: the protein CG file contains TER lines separating the subunits, but the CG .gro file has no TER. > > -Justin > >> >> ; >> ; mod21 | MARTINI 2.1 >> ; >> >> ; Include force field poarameters containing all particle definitions, >> ; the interaction matrix, plus the topology for water. >> >> #include "martini_v2.1.itp" >> >> ; Then include the file(s) containing the topologies of other >> ; molecules present in your system. >> >> ; #include "martini_v2.0_lipids.itp" >> ; #include "martini_v2.0_salt.itp" >> >> >> #include "mod21.itp" >> >> ; Define a name for your system >> >> [ system ] >> mod21 >> >> ; Define the composition of your system >> ; The molecule names should correspond to those defined in the itp >> file(s). >> >> [ molecules ] >> Protein 1 >> ; DPPC 128 >> ; W 2000 >> ; NA+ 20 >> ; CL- 20 >> >> It seems that commenting out ";" is placed correctly. >> >> I am sincerely sorry to bother you again. >> >> francesco >> >> >> With command $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -n -o mod21.cg.tpr NOTE: System has non-zero total charge: -5.00e+01 processing coordinates... Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCQd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCP1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BSP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SSAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCC3 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCN0 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHN0 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHNd - BN0) Warning: atom names in mod21.
[gmx-users] Custom Force Field
Dear All, Hello! I spent the last couple of hours reading the GROMACS manual and trying to get my head around the files. One of the things that I want to do is to use a custom force field for ionic liquids related simulations but I don't seem to be able to find instructions on how to do that (probably very trivial...), is there a way to incorporate that into the pdb2gmx interactive force field selection or can you actually specify the force field that you want to use in the command line? Any help would be much appreciated and thank you very much in advance! Kind regards, Honman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] grompp: no such moleculetype
Francesco Pietra wrote: On Mon, Oct 5, 2009 at 4:39 PM, Justin A. Lemkul wrote: Francesco Pietra wrote: Thanks, and beg pardon for the pedestrian mistake. However, I am not yet out. .tpr not generated With command $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -o mod21.cg.tpr There are: 0 OTHER residues There are: 1270PROTEIN residues There are: 0DNA residues Analysing Protein... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/readir.c, line: 798 Fatal error: Group DPPC not found in indexfile. Maybe you have non-default groups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. As I said before, I am using the mdp file as provided by MARTINI. Then you haven't yet appropriately #included the .itp file for DPPC. As I said, I don't understand why about DPPC. The protein is pure standard amino acids and nothing else. I am trying to get the files for simulation in vacuum. I have reexamined all the stuff and I don't see any allusion to a bilayer, unless that comes from the .mdp file. The .top I used in these last attempts reads: I would suggest looking at the .mdp file; grompp wouldn't be complaining if there wasn't some input file specifying an unknown molecule. -Justin ; ; mod21 | MARTINI 2.1 ; ; Include force field poarameters containing all particle definitions, ; the interaction matrix, plus the topology for water. #include "martini_v2.1.itp" ; Then include the file(s) containing the topologies of other ; molecules present in your system. ; #include "martini_v2.0_lipids.itp" ; #include "martini_v2.0_salt.itp" #include "mod21.itp" ; Define a name for your system [ system ] mod21 ; Define the composition of your system ; The molecule names should correspond to those defined in the itp file(s). [ molecules ] Protein 1 ; DPPC 128 ; W 2000 ; NA+ 20 ; CL- 20 It seems that commenting out ";" is placed correctly. I am sincerely sorry to bother you again. francesco With command $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -n -o mod21.cg.tpr NOTE: System has non-zero total charge: -5.00e+01 processing coordinates... Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCQd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCP1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BSP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SSAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCC3 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCN0 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHN0 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHNd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHNd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSP1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC3) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC4) (more than 20 non-matching atom names) WARNING 2 [file "mod21.cg.top", line 28]: 2875 non-matching atom names atom names from mod21.cg.top will be used atom names from mod21.cg.box.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 2724 # G96ANGLES: 2860 # PDIHS: 328 # IDIHS: 187 # CONSTR: 745 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/gmxlib/futil.c, line: 345 File input/output error: index.ndx == Non-matching because of the many -S-S- bonds? Why asking about index.ndx? Non-matching names occur because MARTINI doesn't assign them correctly in the initial system setup. Using the .top names is fine. The I/O error comes from the fact that you have passed the -n flag to grompp without having index.ndx in the working directory. No
Re: [gmx-users] grompp: no such moleculetype
On Mon, Oct 5, 2009 at 4:39 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> Thanks, and beg pardon for the pedestrian mistake. >> >> However, I am not yet out. .tpr not generated >> >> With command >> >> $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -o >> mod21.cg.tpr >> >> >> There are: 0 OTHER residues >> There are: 1270 PROTEIN residues >> There are: 0 DNA residues >> Analysing Protein... >> >> --- >> Program grompp, VERSION 3.3.3 >> Source code file: ../../../../src/kernel/readir.c, line: 798 >> >> Fatal error: >> Group DPPC not found in indexfile. >> Maybe you have non-default groups in your mdp file, while not using >> the '-n' option of grompp. >> In that case use the '-n' option. >> >> As I said before, I am using the mdp file as provided by MARTINI. >> >> > > Then you haven't yet appropriately #included the .itp file for DPPC. As I said, I don't understand why about DPPC. The protein is pure standard amino acids and nothing else. I am trying to get the files for simulation in vacuum. I have reexamined all the stuff and I don't see any allusion to a bilayer, unless that comes from the .mdp file. The .top I used in these last attempts reads: ; ; mod21 | MARTINI 2.1 ; ; Include force field poarameters containing all particle definitions, ; the interaction matrix, plus the topology for water. #include "martini_v2.1.itp" ; Then include the file(s) containing the topologies of other ; molecules present in your system. ; #include "martini_v2.0_lipids.itp" ; #include "martini_v2.0_salt.itp" #include "mod21.itp" ; Define a name for your system [ system ] mod21 ; Define the composition of your system ; The molecule names should correspond to those defined in the itp file(s). [ molecules ] Protein 1 ; DPPC 128 ; W 2000 ; NA+ 20 ; CL- 20 It seems that commenting out ";" is placed correctly. I am sincerely sorry to bother you again. francesco > >> With command >> >> $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -n >> -o mod21.cg.tpr >> >> NOTE: >> System has non-zero total charge: -5.00e+01 >> >> processing coordinates... >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (BCQd - BN0) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SCAC1 - SC1) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (BCP5 - BN0) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SCP1 - SC1) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (BSP5 - BN0) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SSAC1 - SC1) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (BCP5 - BN0) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SCC3 - SC1) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SCQd - SC2) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (BCP5 - BN0) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SCN0 - SC1) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SCQd - SC2) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (BHN0 - BN0) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (BHNd - BN0) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SHAC1 - SC1) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (BHNd - BN0) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SHSC4 - SC2) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SHSP1 - SC1) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SHSC4 - SC3) >> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match >> (SHSC4 - SC4) >> (more than 20 non-matching atom names) >> WARNING 2 [file "mod21.cg.top", line 28]: >> 2875 non-matching atom names >> atom names from mod21.cg.top will be used >> atom names from mod21.cg.box.gro will be ignored >> >> double-checking input for internal consistency... >> renumbering atomtypes... >> converting bonded parameters... >> # BONDS: 2724 >> # G96ANGLES: 2860 >> # PDIHS: 328 >> # IDIHS: 187 >> # CONSTR: 745 >> Walking down the molecule graph to make shake-blocks >> initialising group options... >> processing index file... >> >> --- >> Program grompp, VERSION 3.3.3 >> Source code file: ../../../../src/gmxlib/futil.c, line: 345 >> >> File input/output error: >> index.ndx >> == >> Non-matching because of the many -S-S- bonds? Why asking about index.ndx? >> > > Non-matching names occur because MARTINI doesn't assign them correctly in > the initial system setup. Using the .top names is fine. >
RE: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem
Hi, I came back to my original stretching potential in tabulated form and I have still problems... when running a geometry optimization the results are like that: **+ ^MStep 635, Epot=2.259501e+02, Fnorm=4.086e+00, Fmax=1.886e+01 (atom 34) ^MStep 636, Epot=2.259499e+02, Fnorm=3.847e+00, Fmax=1.992e+01 (atom 33) ^MStep 637, Epot=2.259495e+02, Fnorm=1.002e+01, Fmax=5.408e+01 (atom 33) ^MStep 638, Epot=2.259449e+02, Fnorm=1.026e+01, Fmax=4.098e+01 (atom 34) ^MStep 639, Epot=2.259393e+02, Fnorm=2.193e+01, Fmax=1.159e+02 (atom 35) ^MStep 640, Epot=2.259364e+02, Fnorm=1.469e+01, Fmax=7.064e+01 (atom 34) ^MStep 641, Epot=2.259335e+02, Fnorm=1.281e+01, Fmax=7.154e+01 (atom 34) ^MStep 642, Epot=2.259315e+02, Fnorm=5.803e+00, Fmax=2.861e+01 (atom 35) ^MStep 643, Epot=2.259314e+02, Fnorm=6.332e+00, Fmax=3.116e+01 (atom 34) ^MStep 644, Epot=2.259310e+02, Fnorm=3.550e+00, Fmax=1.502e+01 (atom 34) Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 0.1 as if the system is frozen. My system here is an isolated, linear and finite-length chain. When running an md simulation I got the error: --- Program mdrun_mpi, VERSION 4.0.5 Source code file: bondfree.c, line: 1772 Fatal error: A tabulated bond interaction table number 0 is out of the table range: r 1.815411, between table indices 1815 and 1816, table length 1001 --- The tabulated potential is uniformly spaced, the bond type is 8 to exclude LJ interaction between bonded atoms, nrexcl=1 to include 1-3 interactions (as required by MARTINI force field). The same system does not have any problem when running simulation with an harmonic stretching potential in both numerical and analytical form. Does anyone have any suggestion for possible solutions or error in the input? Thanks AM Messaggio originale Da: g...@hotmail.com Data: 2-ott-2009 2.29 PM A: "Discussion list for GROMACS users" Ogg: RE: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem --> Hi, As I (and Mark) said, the spacing "should be" equal. If not, correct results are not guaranteed. grompp simply assumes dx is the last x divided by n-1. For Gromacs 4.1 I have put a check in grompp. If two consecutive delta x's differ by more than 1% you get a fatal error and you can not proceed. Berk Date: Fri, 2 Oct 2009 16:09:55 +0200 From: albita...@virgilio.it To: gmx-users@gromacs.org Subject: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem CC: g...@hotmail.com Hi Berk, I repeated the calculations with a perfectly uniformly spaced numerical potential. The results are now consistent with those obtained by using the same potential but in analytical form. As a check, I also carried out a simple optimization with the same numerical potential but removing some points here and there. The effect on the energies is quite large! This means that if there is just a minimal imperfection in the table spacing the results of the calculation are largely affected. For this reason I suggest you to add in grompp , if possible, a check for the points spacing which prints an error warning when it is not uniform. Thank you for your help and disposition. Alberto Messaggio originale Da: g...@hotmail.com Data: 1-ott-2009 3.23 PM A: "Discussion list for GROMACS users" Ogg: RE: R: RE: R: RE: R: RE: R: RE: R: RE: R: Re: R:[gmx-users] Tabulated potential - Problem Ah, I thought the sentence in one of my previous mails was clear enough: "The points in the table_b.xvg file should be equally spaced. grompp assumes equal spacing, but does not check this." I think "should be" and "must be" are equivalent in this context. But we can clarify the manual, and add a check in grompp. But at the connecting point the potentials should be equal by definition, right? Anyhow, for numerical work you should smooth you potentials in some way. You can do this and generate a lot of extra (intermediate, smoothed) points or use a small amount of points. But in the end they should be equally spaced for computational efficiency. mdrun could, in principle, also do this job, but it is better if the user thinks about this. Berk Date: Thu, 1 Oct 2009 17:13:30 +0200 From: albita...@virgilio.it To: g...@hotmail.com Subject: R: RE: R: RE: R: RE: R: RE: R: RE: R: Re: R:[gmx-users] Tabulated potential- Problem Yes I know about it. This is the reason for my previous questions if "should be uniformly spaced" means indeed "must be equally spaced". When generating a numerical potential from boltzmann inversion I need to "complete" on a wider range of distance with the left and right repulsive branches. At the connecting points of the different b
Re: [gmx-users] grompp: no such moleculetype
Francesco Pietra wrote: Thanks, and beg pardon for the pedestrian mistake. However, I am not yet out. .tpr not generated With command $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -o mod21.cg.tpr There are: 0 OTHER residues There are: 1270PROTEIN residues There are: 0DNA residues Analysing Protein... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/readir.c, line: 798 Fatal error: Group DPPC not found in indexfile. Maybe you have non-default groups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. As I said before, I am using the mdp file as provided by MARTINI. Then you haven't yet appropriately #included the .itp file for DPPC. With command $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -n -o mod21.cg.tpr NOTE: System has non-zero total charge: -5.00e+01 processing coordinates... Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCQd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCP1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BSP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SSAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCC3 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCN0 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHN0 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHNd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHNd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSP1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC3) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC4) (more than 20 non-matching atom names) WARNING 2 [file "mod21.cg.top", line 28]: 2875 non-matching atom names atom names from mod21.cg.top will be used atom names from mod21.cg.box.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 2724 # G96ANGLES: 2860 # PDIHS: 328 # IDIHS: 187 # CONSTR: 745 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/gmxlib/futil.c, line: 345 File input/output error: index.ndx == Non-matching because of the many -S-S- bonds? Why asking about index.ndx? Non-matching names occur because MARTINI doesn't assign them correctly in the initial system setup. Using the .top names is fine. The I/O error comes from the fact that you have passed the -n flag to grompp without having index.ndx in the working directory. Note that having an index file doesn't necessarily solve your problem; the warning is printed in case you have non-default groups for, e.g., T-coupling or energygrps. If you have a "moleculetype not found," then you haven't #included the .itp file and an index file won't save you. -Justin Thanks for help francesco On Mon, Oct 5, 2009 at 12:33 PM, Justin A. Lemkul wrote: Francesco Pietra wrote: Hi: As I found it difficult to manage solvation - the way I would like - with a pore protein (a trimer) partly immersed into a bilayer, I started with the protein alone in vacuum, in order to try to fix the problems step-by-step. Unfortunately, I can't fix simple problems with grompp. 1) Generated mod21.itp from mod21.pdb 2) Generated mod21.cg.pdb with awk script) 3) editconf -f mod21.cg.pdb -o mod21.cg.gro 4) genbox -cp mod21.cg.gro -box 10 17 10 -o mod21.cg.box.gro 5) grompp -np 4 -f mod21.cg.box.mdp -c mod21.cg.box.gro -p mod21.cg.box.top -warnmax 10 Error: no such moleculetype Protein. . .mdp is merely a renamed martini_v2.0.example.mdp, taking care that "cpp = /usr/bin/cpp". .top was from editing martini_v2.0.example.top and reads (in between ===): == ; ; mod21 | MARTINI 2.1 ; ; Include force fi
Re: [gmx-users] grompp: no such moleculetype
Thanks, and beg pardon for the pedestrian mistake. However, I am not yet out. .tpr not generated With command $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -o mod21.cg.tpr There are: 0 OTHER residues There are: 1270PROTEIN residues There are: 0DNA residues Analysing Protein... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/readir.c, line: 798 Fatal error: Group DPPC not found in indexfile. Maybe you have non-default groups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. As I said before, I am using the mdp file as provided by MARTINI. With command $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -n -o mod21.cg.tpr NOTE: System has non-zero total charge: -5.00e+01 processing coordinates... Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCQd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCP1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BSP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SSAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCC3 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCN0 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHN0 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHNd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHNd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSP1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC3) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC4) (more than 20 non-matching atom names) WARNING 2 [file "mod21.cg.top", line 28]: 2875 non-matching atom names atom names from mod21.cg.top will be used atom names from mod21.cg.box.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 2724 # G96ANGLES: 2860 # PDIHS: 328 # IDIHS: 187 # CONSTR: 745 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/gmxlib/futil.c, line: 345 File input/output error: index.ndx == Non-matching because of the many -S-S- bonds? Why asking about index.ndx? Thanks for help francesco On Mon, Oct 5, 2009 at 12:33 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> Hi: >> >> As I found it difficult to manage solvation - the way I would like - >> with a pore protein (a trimer) partly immersed into a bilayer, I >> started with the protein alone in vacuum, in order to try to fix the >> problems step-by-step. Unfortunately, I can't fix simple problems with >> grompp. >> >> 1) Generated mod21.itp from mod21.pdb >> >> 2) Generated mod21.cg.pdb with awk script) >> >> 3) editconf -f mod21.cg.pdb -o mod21.cg.gro >> >> 4) genbox -cp mod21.cg.gro -box 10 17 10 -o mod21.cg.box.gro >> >> 5) grompp -np 4 -f mod21.cg.box.mdp -c mod21.cg.box.gro -p >> mod21.cg.box.top -warnmax 10 >> >> Error: no such moleculetype Protein. >> >> . >> .mdp is merely a renamed martini_v2.0.example.mdp, taking care that >> "cpp = /usr/bin/cpp". >> >> .top was from editing martini_v2.0.example.top and reads (in between ===): >> == >> ; >> ; mod21 | MARTINI 2.1 >> ; >> >> ; Include force field parameters containing all particle definitions, >> ; the interaction matrix, plus the topology for water. >> >> #include "martini_v2.1.itp" >> >> ; Then include the file(s) containing the topologies of other >> ; molecules present in your system. >> >> ; #include "martini_v2.0_lipids.itp" >> ; #include "martini_v2.0_salt.itp" >> >> #include mod21.itp >> > > This #include statement has the wrong syntax. See any of the above for the > correct way to do it. > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS D
Re: [gmx-users] Installation error (gromac4.0.5)
Nkwe Monama wrote: Dear all, I have been trying to install gromacs on my IBM E1350 linux cluster (amd86_64). I've managed to run cofigure without any error but I get the following error during make step. mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/CHPC/home/chpc/Test/oscar/gromacs-4.0.5/share/top\" -I/CHPC/home/chpc/Test/oscar/fftw-3.1.3/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -std=gnu99 -MT grompp.o -MD -MP -MF .deps/grompp.Tpo -c -o grompp.o grompp.c mv -f .deps/grompp.Tpo .deps/grompp.Po /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -std=gnu99 -L//CHPC/home/chpc/Test/oscar/fftw-3.1.3/lib -o grompp grompp.o libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la -L/usr/X11/lib -lnsl -lfftw3f -lm -lX11 mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -std=gnu99 -o grompp grompp.o -L//CHPC/home/chpc/Test/oscar/fftw-3.1.3/lib ./.libs/libgmxpreprocess_mpi.a -L/usr/X11/lib ../mdlib/.libs/libmd_mpi.a /CHPC/home/chpc/Test/oscar/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a ../gmxlib/.libs/libgmx_mpi.a -lnsl /CHPC/home/chpc/Test/oscar/fftw-3.1.3/lib/libfftw3f.a -lm -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/X11/lib/libX11.so when searching for -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/X11/lib/libX11.a when searching for -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/X11/lib/libX11.so when searching for -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/X11/lib/libX11.a when searching for -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: cannot find -lX11 collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/CHPC/home/chpc/Test/oscar/gromacs-4.0.5/src/kernel' make[2]: *** [all-recursive] Error 1 Please help. Having you tried configuring --without-x ? -Justin Regards, Nkwe -- 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://lists.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] 256 DPPC bilayer
ram bio wrote: Dear Gromacs Users, I am looking for a DPPC bilayer system of 256 and above , can anybody suugest me the site from where I can download Please... Take a pre-equilibrated 128 DPPC bilayer from any number of sites and use genconf or genbox. -Justin Thanks Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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://lists.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] Installation error (gromac4.0.5)
Dear all, I have been trying to install gromacs on my IBM E1350 linux cluster (amd86_64). I've managed to run cofigure without any error but I get the following error during make step. mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/CHPC/home/chpc/Test/oscar/gromacs-4.0.5/share/top\" -I/CHPC/home/chpc/Test/oscar/fftw-3.1.3/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -std=gnu99 -MT grompp.o -MD -MP -MF .deps/grompp.Tpo -c -o grompp.o grompp.c mv -f .deps/grompp.Tpo .deps/grompp.Po /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -std=gnu99 -L//CHPC/home/chpc/Test/oscar/fftw-3.1.3/lib -o grompp grompp.o libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la -L/usr/X11/lib -lnsl -lfftw3f -lm -lX11 mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -std=gnu99 -o grompp grompp.o -L//CHPC/home/chpc/Test/oscar/fftw-3.1.3/lib ./.libs/libgmxpreprocess_mpi.a -L/usr/X11/lib ../mdlib/.libs/libmd_mpi.a /CHPC/home/chpc/Test/oscar/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a ../gmxlib/.libs/libgmx_mpi.a -lnsl /CHPC/home/chpc/Test/oscar/fftw-3.1.3/lib/libfftw3f.a -lm -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/X11/lib/libX11.so when searching for -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/X11/lib/libX11.a when searching for -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/X11/lib/libX11.so when searching for -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/X11/lib/libX11.a when searching for -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: cannot find -lX11 collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/CHPC/home/chpc/Test/oscar/gromacs-4.0.5/src/kernel' make[2]: *** [all-recursive] Error 1 Please help. Regards, Nkwe -- This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html. This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. MailScanner thanks Transtec Computers for their support. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] 256 DPPC bilayer
Dear Gromacs Users, I am looking for a DPPC bilayer system of 256 and above , can anybody suugest me the site from where I can download Please... Thanks Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Exclusion and 1-4 interactions with tabulated potential
Johannes Kamp wrote: Hi @ all, I'm a little confused about 1-4 interactions at the moment and I hope you can help me along... I'm using tabulated potentials for bonded and non-bonded potentials with the Martini FF. The 1-4 interactions are fully represented by the non-bonded potential, Rather than "fully", if they're "only" represented with the non-bonded potential, then you merely have to address whether they're scaled or not. The "generate pairs" mechanism is useful in the former case - it generates a list of atom pairs for which the nonbonded interactions are generated from the usual potential scaled by the fudge factors, except that [pairs] specified in the .top are not over-ridden. Presumably nrexcl = 3 directs pair generation for 1-4 interactions... I'd guess nrexcl = 2 might direct pair generation for 1-3... charged particles are not present. I implemented the non-bonded potential with -table option in mdrun. After reading chapter 4.6.1 and 5.7.1 of the manual about exclusion and 1-4 interactions the following confused me: I set the neighbor exclusion nrexcl = 3. Is that correct if I've got the 1-4 interactions represented in my non-bonded potential, or do I have to set nrexcl = 2? nrexcl = 3 means no 1-4 interactions are generated (see for example footnote to table 5.3 in 5.7.1). If you wanted them, either in normal or scaled form, you'd have to supply them in a separate pair list, or use nrexcl = 2. The third para of 4.6.1 says this. Furthermore in chapter 4.6.1 something is said about a reducing factor of two, do I have to use it? -I'm asking because in my simulations everything clots together, thus the nb Forces seem to be too strong. Read the forcefield paper/documentation/whatever to find the answer this. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Exclusion and 1-4 interactions with tabulated potential
Hi @ all, I'm a little confused about 1-4 interactions at the moment and I hope you can help me along... I'm using tabulated potentials for bonded and non-bonded potentials with the Martini FF. The 1-4 interactions are fully represented by the non-bonded potential, charged particles are not present. I implemented the non-bonded potential with -table option in mdrun. After reading chapter 4.6.1 and 5.7.1 of the manual about exclusion and 1-4 interactions the following confused me: I set the neighbor exclusion nrexcl = 3. Is that correct if I've got the 1-4 interactions represented in my non-bonded potential, or do I have to set nrexcl = 2? Furthermore in chapter 4.6.1 something is said about a reducing factor of two, do I have to use it? -I'm asking because in my simulations everything clots together, thus the nb Forces seem to be too strong. Regards, Johannes ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] size dependence of fluctuations
Zuzana Benkova wrote: Dear GROMACS users, most likely I am asking a trivial question but I need to be sure about it for calculations of heat capacity based on the fluctuations of energy in canonical ensemble. I am doing simulation of water using TIP4P model. I compare two systems consisting of 216 and 8*216 = 1728 molecules. The expected fluctuations for the larger system should be reduced 8^(1/2)=2.83 times with respect to the fluctuations of the smaller system. Actually, this applies only to the fluctuations in intensive properties such as the temperature, pressure and density while the fluctuations in extensive properties such as energies exceed about 2.83 times the corresponding fluctuations for smaller system. Could you explain me the inverse ratio of fluctuations? Have you simulated long enough that you can measure these fluctuations reliably? Look at the trend in their behaviour with increasing time. I have also one question regarding the heat capacity calculation. If I want to apply the formula for canonical ensemble (-^2)/(kbT^2) than the capacity should be size dependent. I am a bit puzzled about it and any explanation would be very helpful for me. Thanks in advance Heat capacity is extensive. Quoting the output that's confusing you would help you get better feedback. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] [Gromacs 3.3.3] tests for parallel - is this reasonable?
Thomas Schlesier wrote: Hi all, Why use 3.3.3? For most purposes the most recent version is more reliable and much faster. i have done some small tests for parallel calculations with different systems: All simulations were done on my laptop which has a dualcore CPU. (1) 895 waters - 2685 atoms, for 5 steps (100ps) cutoffs 1.0nm (no pme); 3nm cubic box Nobody uses cutoffs any more. Test with the method you'll use in real calculation - PME. single: NODE (s) Real (s) (%) Time:221.760222.000 99.9 3:41 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 13.913 3.648 38.961 0.616 parallel (2 cores): NODE (s) Real (s) (%) Time:160.000160.000100.0 2:40 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 19.283 5.056 54.000 0.444 Total Scaling: 98% of max performance => 1.386 times faster (2) 3009 waters - 9027 atoms, for 5 steps (100ps) cutoffs 1.0nm (no pme); 4.5nm cubic box single: NODE (s) Real (s) (%) Time:747.830751.000 99.6 12:27 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 13.819 3.617 11.553 2.077 parallel (2cores): NODE (s) Real (s) (%) Time:525.000525.000100.0 8:45 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 19.684 5.154 16.457 1.458 Total Scaling: 98% of max performance => 1.424 times faster (3) 2 waters rest same as (1) single: NODE (s) Real (s) (%) Time: 0.680 1.000 68.0 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 0.012167.973 12705.884 0.002 parallel: NODE (s) Real (s) (%) Time: 9.000 9.000100.0 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 0.003 17.870960.000 0.025 Total Scaling: 88% of max performance => about 10 times slower (this one was more a test to see how the values look for a case where parallelisation is a waste) So now my questions: 1) Are the values reasonable (i mean not really each value, but more the speed difference between parallel and single)? I would have assumed that if the system is big (2) i'm with two cores about a factor of a little bit less then 2 faster, and not only around 1.4 times It depends on a whole pile of factors. Are your cores real or only hyperthreads? Do they share caches? I/O systems? Can MPI use the cache for communication or does it have to write through to main memory? How big are the caches? People's laptops that were designed for websurfing and editing Word documents often skimp on stuff that is necessary if you're actually planning to keep your floating point units saturated with work... You may like to run two copies of the same single-processor job to get a handle on these issues. 2) In the md0.log files (for parallel runs) i have seen for all three simulations the following line: "Load imbalance reduced performance to 200% of max" What does it mean? And why is it in all three cases the same? Dunno, probably buggy. 3) What does the "Total Scaling" mean? In case (3) i'm with single 10 times better, but for parallel it says i have 88% of max performance (If i set single to 100%, it would only be 10% performance). The spatial decomposition will not always lead to even load balance. That's life. The domain decomposition in 4.x will do a much better job, though it's probably not going to matter much for 2 cores on small systems and short runs. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] option for finding forces between two groups
Pradip Biswas wrote: Hi, Anyone can please tell me whether there is any option in GROMACS to find forces between two groups (say for example, between two residues in a protein or between a peptide and a residue in a Protein for Protein-peptide interaction) or one need to workaround with the code to get that? Probably you should do a rerun with energy group exclusions used properly. See section 7.3 of the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] error coordinates in .gro donnot match .top
Asmaa Elsheshiny wrote: Hi, all when I want to use gromacs preprocessor grompp to obtain .tpr to use in the energy minimization as follow grompp -f minim.mdp -c bradywaterbox.gro -p brady.top -o minimbrady.tpr I got the following error message Fatal error: number of coordinates in coordinate file (bradywaterbox.gro, 670) does not match topology (brady.top, 0) where, bradywaterbox.gro & brady.top are obtained from genbox -cp solvatedbrady.gro -cs spc216.gro -o bradywaterbox.gro -p brady.top I think that the topology file didnot include the solvent molecules so it canont be mached with the coordinate file .gro , did it? So how can I fix this problem? There is a section regarding this error here: http://www.gromacs.org/Documentation/Errors grompp doesn't seem to think your topology has anything in it at all, so it's not simply an issue of the waters. -Justin Regards, Asmaa ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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://lists.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] grompp: no such moleculetype
Francesco Pietra wrote: Hi: As I found it difficult to manage solvation - the way I would like - with a pore protein (a trimer) partly immersed into a bilayer, I started with the protein alone in vacuum, in order to try to fix the problems step-by-step. Unfortunately, I can't fix simple problems with grompp. 1) Generated mod21.itp from mod21.pdb 2) Generated mod21.cg.pdb with awk script) 3) editconf -f mod21.cg.pdb -o mod21.cg.gro 4) genbox -cp mod21.cg.gro -box 10 17 10 -o mod21.cg.box.gro 5) grompp -np 4 -f mod21.cg.box.mdp -c mod21.cg.box.gro -p mod21.cg.box.top -warnmax 10 Error: no such moleculetype Protein. . .mdp is merely a renamed martini_v2.0.example.mdp, taking care that "cpp = /usr/bin/cpp". .top was from editing martini_v2.0.example.top and reads (in between ===): == ; ; mod21 | MARTINI 2.1 ; ; Include force field parameters containing all particle definitions, ; the interaction matrix, plus the topology for water. #include "martini_v2.1.itp" ; Then include the file(s) containing the topologies of other ; molecules present in your system. ; #include "martini_v2.0_lipids.itp" ; #include "martini_v2.0_salt.itp" #include mod21.itp This #include statement has the wrong syntax. See any of the above for the correct way to do it. -Justin -- 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://lists.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] error coordinates in .gro donnot match .top
Hi, all when I want to use gromacs preprocessor grompp to obtain .tpr to use in the energy minimization as follow grompp -f minim.mdp -c bradywaterbox.gro -p brady.top -o minimbrady.tpr I got the following error message Fatal error: number of coordinates in coordinate file (bradywaterbox.gro, 670) does not match topology (brady.top, 0) where, bradywaterbox.gro & brady.top are obtained from genbox -cp solvatedbrady.gro -cs spc216.gro -o bradywaterbox.gro -p brady.top I think that the topology file didnot include the solvent molecules so it canont be mached with the coordinate file .gro , did it? So how can I fix this problem? Regards, Asmaa ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Making Commands Non-Interactive
Cool. You can also write a python script to generate and execute your
C-code, which you then wrap with Java to be executed through Ruby...
etc. Erik, can you maybe give the assembly solution?
:p
Tsjerk
On Mon, Oct 5, 2009 at 10:15 AM, Alexander Bujotzek wrote:
> I once wrote some lines of adventurous C-code to get an observable of
> choice from g_energy without typing the observable index myself... this
> may also be applied to trjconv I think.
>
> string genergyCall = "g_energy -f " + myEdrFile + " -o " + myXvgFile + "
> &> /dev/null";
> string energyObs = "8"; // e.g. potential
>
> FILE *fpipe;
> fpipe = popen(genergyCall.c_str(),"w");
> fwrite(energyObs.data(), 1, 1, fpipe); // tell g_energy what to write
> pclose(fpipe);
>
> If you want to pipe more stuff to the program you are calling, the buffer
> size of fwrite has to be increased.
> So you might put this into a minimal C-program and start that
> non-interactive with qsub or whatever.
>
>
>> Dear GMX Users,
>>
>> I ask this question in this mailing list since probably a user have
>> already encountered this similar problem. I would like to post-process my
>> trajectory with the command trjconv (in mpi mode). For this I use the
>> following shell command:
>>
>> echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi
>> -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o
>> ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0
>> ("System")
>>
>> It works but since my simulations is very long (> 300ns) the command stops
>> in the middle of the trajectory before to finish the process ( i suspect a
>> time limit for using the interactive mode). So i would like to use a
>> script to do the task. How to pass the choice 0 in the script (i.e.
>> equivalent to the echo 0). I use a bash shell and the command qsub to
>> launch a mpi job.
>>
>> I have tried to adapt the examples available in the GMX website with a
>> text file as suggested by the author in GROMACS site with no success.
>>
>> Thank you again for your help
>>
>> ___
>> gmx-users mailing list gmx-us...@gromacs.org
>> http://lists.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
>
>
> --
> Alexander Bujotzek
> Zuse Institute Berlin
> Computational Drug Design Group
> Tel. : +49 30 84185-234
> eMail: bujot...@zib.de
> ___
> gmx-users mailing list gmx-us...@gromacs.org
> http://lists.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
___
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Re: [gmx-users] Making Commands Non-Interactive
Have you tried:
echo 0 > zero
trjconv bla bla bla < zero
You could put more arguments in the file, for example - use the "-center"
option, and then echo another 0 into the zero file.
--Omer.
On Sun, Oct 4, 2009 at 18:22, ABEL Stephane 175950 wrote:
> Dear GMX Users,
>
> echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi
> -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o
> ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0
> ("System")
>
>
___
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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Making Commands Non-Interactive
I once wrote some lines of adventurous C-code to get an observable of
choice from g_energy without typing the observable index myself... this
may also be applied to trjconv I think.
string genergyCall = "g_energy -f " + myEdrFile + " -o " + myXvgFile + "
&> /dev/null";
string energyObs = "8"; // e.g. potential
FILE *fpipe;
fpipe = popen(genergyCall.c_str(),"w");
fwrite(energyObs.data(), 1, 1, fpipe); // tell g_energy what to write
pclose(fpipe);
If you want to pipe more stuff to the program you are calling, the buffer
size of fwrite has to be increased.
So you might put this into a minimal C-program and start that
non-interactive with qsub or whatever.
> Dear GMX Users,
>
> I ask this question in this mailing list since probably a user have
> already encountered this similar problem. I would like to post-process my
> trajectory with the command trjconv (in mpi mode). For this I use the
> following shell command:
>
> echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi
> -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o
> ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0
> ("System")
>
> It works but since my simulations is very long (> 300ns) the command stops
> in the middle of the trajectory before to finish the process ( i suspect a
> time limit for using the interactive mode). So i would like to use a
> script to do the task. How to pass the choice 0 in the script (i.e.
> equivalent to the echo 0). I use a bash shell and the command qsub to
> launch a mpi job.
>
> I have tried to adapt the examples available in the GMX website with a
> text file as suggested by the author in GROMACS site with no success.
>
> Thank you again for your help
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.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
--
Alexander Bujotzek
Zuse Institute Berlin
Computational Drug Design Group
Tel. : +49 30 84185-234
eMail: bujot...@zib.de
___
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[gmx-users] grompp: no such moleculetype
Hi: As I found it difficult to manage solvation - the way I would like - with a pore protein (a trimer) partly immersed into a bilayer, I started with the protein alone in vacuum, in order to try to fix the problems step-by-step. Unfortunately, I can't fix simple problems with grompp. 1) Generated mod21.itp from mod21.pdb 2) Generated mod21.cg.pdb with awk script) 3) editconf -f mod21.cg.pdb -o mod21.cg.gro 4) genbox -cp mod21.cg.gro -box 10 17 10 -o mod21.cg.box.gro 5) grompp -np 4 -f mod21.cg.box.mdp -c mod21.cg.box.gro -p mod21.cg.box.top -warnmax 10 Error: no such moleculetype Protein. . .mdp is merely a renamed martini_v2.0.example.mdp, taking care that "cpp = /usr/bin/cpp". .top was from editing martini_v2.0.example.top and reads (in between ===): == ; ; mod21 | MARTINI 2.1 ; ; Include force field parameters containing all particle definitions, ; the interaction matrix, plus the topology for water. #include "martini_v2.1.itp" ; Then include the file(s) containing the topologies of other ; molecules present in your system. ; #include "martini_v2.0_lipids.itp" ; #include "martini_v2.0_salt.itp" #include mod21.itp ; Define a name for your system [ system ] mod21 ; Define the composition of your system ; The molecule names should correspond to those defined in the itp file(s). [ molecules ] Protein 1 ; DPPC 128 ; W 2000 ; NA+ 20 ; CL- 20 === Correspondingly, mod21.cg.box.gro reads: = Great Red Oystrich Makes All Chemists Sane 2875 1LEUBN01 15.604 6.397 9.477 1LEUSC12 15.848 6.475 9.463 2SERBN03 15.784 6.086 9.582 2SERSC14 15.874 6.060 9.703 ... 1270TYRBN0 2872 14.759 6.270 10.494 1270TYRSC1 2873 14.668 6.105 10.342 1270TYRSC2 2874 14.442 6.038 10.300 1270TYRSC3 2875 14.607 5.874 10.352 10.0 17.0 10.0 = and mod21.itp file reads: ;;; MARTINI 2.1 coarse-grained topology ;;; Generated by seq2itp.pl version 1.1.2 ;;; SEQ: LSLKRALWAL . [moleculetype] ;molnameexclusions Protein 1 [atoms] 1 Qd 1 LEU BCQd1 1.000 ; COI 2 AC1 1 LEU SCAC1 2 0.000 ; COI ... ... [ bonds ] ;backbone-backbone bonds 1 3 1 0.350 400 ; COI-COI .. ... 287128721 0.350 400 ; HLX-COI ;backbone-sidechain bonds 1 2 1 0.330 7500; LEU1 ... ... 287228731 0.320 5000; TYR1270 ;sc1-sc2 bonds (ARG, LYS) 8 9 1 0.280 5000; LYS4 .. ... 280628071 0.280 5000; LYS1236 ;short elastic bonds 85 91 1 0.640 2500; HIS35-THR37 ... .. 280028051 0.640 2500; GLN1234-LYS1236 ;long elastic bonds 85 93 1 0.970 2500; HIS35-LYS38 .. 279828051 0.970 2500; GLU1233-LYS1236 [ constraints ] ;sc-sc constraints (Ring Structures) 17 18 1 0.270 ; TRP8 287428751 0.270 ; TYR1270 ;bc-sc constraints (ITV) 38 39 1 0.265 ; VAL18 . 285328541 0.265 ; VAL1262 [angles] ;backbone-backbone-backbone angles 1 3 5 2 127.00 25 ; COI-COI-BND ... .. 2867287128722 96.00 700 ; HLX-HLX-COI ;backbone-backbone-sidechain angles 3 1 2 2 100.00 25 ; COI-LEU1 .. ... 2871287228732 100.00 25 ; HLX-TYR1270 ;backbone-sidechain-sidechain angles (ARG and RINGS) 7 8 9 2 180.00 25 ; LYS4 .. ... 2872287328752 150.00 50 ; TYR1270 [dihedrals] ;improper dihedral angles 16 18 19 17 2 0.0050 ; TRP8 . 28722874287528732 0.0050 ; TYR1270 ;proper dihedral angles ;helix backbone dihedrals 13 14 16 21 1 -120.00 400 1 ; LEU7 ... .. 28592861286528671 -120.00 400 1 ; PHE1266 28612865286728711 -120.00 400 1 ; ASP1267 I am aware that the structure fil
