[gmx-users] help on Graphene Nano Sheets
I am still in trouble with Graphene layers. I study come aspects about bond, dihedral and improper dihedral from blog and manuals. My layer of grafene, and my nanotube still go to collapse, during a em simulation. I did not find nothing about the all_dihedral parameter in bondedtype, in rpt file, I try to copy my force field set suggested from Minoia in all itp files: forcefield ffbonded and ffnonbonded, i try to change parameters in dihedrals from 1 to 3, and in RemoveDih from 0 to 1. I try to add periodic_molecules=yes in mdp file, but i am still away from my goal. Sorry Alex, you said that i don't have to change the dihedrals from 1 to 3 in the top file, but with if i don't change it i always get the error: No default Proper Dih. types, for all 168 dihedrals, also you suggest to add something in ffbonded.itp but i don't know what. An other thing that i want to try is to block one side of the graphene layer, i was surfing on line and i find this: [ moleculetype] This_one [ position_restraints ] ; ai funct fcxfcyfcz 111000 1000 1000 ; restrains to a point 211000 0 1000 ; restrains to a line (y-axis) 211000 0 0 ; restrains to a plane (y-z-plane) so that means that i have to call differently the atoms that are in the bourdary side that i want block? How i can choose the parameters fcx fcy and fcz? what these value stand for? Bests. Il 24/04/2015 18:45, Alex ha scritto: Andrea Minoia's tutorial describes the setup of angles, which in the case of graphene, is extremely simple from the geometry standpoint. There is no need for chancing, just add the proper entries under [dihedraltypes] in ffbonded.itp, x2top will take care of the rest. It's also a pretty good idea to actually read the manual on the definition of angles and dihedrals. Energy minimization destroys the sheet, because there's a mess in your setup. Alex MC Hi people, MC I was able to run the graphene layer sheet, by follow your advices. MC I had a problem with the dihetral angle, MC i solved it by chancing, im the top file the funct parameter from 1 to MC 3, as reported in bold below, MC . MC [ dihedrals ] MC ; aiajakal functc0c1 c2 MC c3c4c5 MC 6 1 2 3 *3 * MC 2 1 6 5 *3 * MC 2 18887 *3* MC 1 2 3 4 *3 * MC ... MC and also, by changing in rtp files all_dihedrals from 1 to 0, MC .. MC [ bondedtypes ] MC ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih MC 1 1 3 1 *0* 3 1 0 MC .. MC But, when i run the mdrun file, after the minimizzation, the model MC result destroyer, all the atom of graphene are spreads arround monitor, MC and they are not yet connected as in the original geometry. MC I would like to have some advices. What is wrong? how i have to set the MC dihedral angles? MC Thanks. MC Il 23/04/2015 20:04, abhijit Kayal ha scritto: Hi Mercelo Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C 612.01100 0.000 A3.4e-01 3.61200e-01 Then in atomname2type.n2t file add the following lines. Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Then use g_x2top. This will work. On Thu, Apr 23, 2015 at 10:54 PM, Alex nedoma...@gmail.com wrote: I think we've covered this when I was having the same issue. If you're trying to simulate a multi-molecule system, then just copy the entire forcefield .ff folder to your local directory and modify the following files: ffbonded.itp ffnonbonded.itp atomnames2types.n2t No need to create rtp entries for graphene/nanotubes, so you can ignore that part of Andrea's tutorial. Instead of just C in his tutorial, come up with a unique label to avoid conflicts, which should then also be used in your PDB. Then what I would do is create a topology entry for just graphene and convert it to a stand-alone itp by stripping off system definitions. This is basically opening the top file, removing those definitions and resaving as *.itp. After that, you can just use pdb2gmx on the remaining parts of the system and complete the system topology by hand. I know, this sounds like a lot of manual tweaking, but this is the paradigm. Good luck! Alex MC I run a graphene nanolayer, usin the below description (from previous mail. MC Now i got an other error. It look like there is a conflict in a force MC field system, someone can suggest me how to modify it? MC the force field file came from Minoia advices, reported
[gmx-users] help on Graphene Nano Sheets
Hi people, I was able to run the graphene layer sheet, by follow your advices. I had a problem with the dihetral angle, i solved it by chancing, im the top file the funct parameter from 1 to 3, as reported in bold below, . [ dihedrals ] ; aiajakal functc0c1 c2 c3c4c5 6 1 2 3 *3 * 2 1 6 5 *3 * 2 18887 *3* 1 2 3 4 *3 * ... and also, by changing in rtp files all_dihedrals from 1 to 0, .. [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1 3 1 *0* 3 1 0 .. But, when i run the mdrun file, after the minimizzation, the model result destroyer, all the atom of graphene are spreads arround monitor, and they are not yet connected as in the original geometry. I would like to have some advices. What is wrong? how i have to set the dihedral angles? Thanks. Il 23/04/2015 20:04, abhijit Kayal ha scritto: Hi Mercelo Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C 612.01100 0.000 A3.4e-01 3.61200e-01 Then in atomname2type.n2t file add the following lines. Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Then use g_x2top. This will work. On Thu, Apr 23, 2015 at 10:54 PM, Alex nedoma...@gmail.com wrote: I think we've covered this when I was having the same issue. If you're trying to simulate a multi-molecule system, then just copy the entire forcefield .ff folder to your local directory and modify the following files: ffbonded.itp ffnonbonded.itp atomnames2types.n2t No need to create rtp entries for graphene/nanotubes, so you can ignore that part of Andrea's tutorial. Instead of just C in his tutorial, come up with a unique label to avoid conflicts, which should then also be used in your PDB. Then what I would do is create a topology entry for just graphene and convert it to a stand-alone itp by stripping off system definitions. This is basically opening the top file, removing those definitions and resaving as *.itp. After that, you can just use pdb2gmx on the remaining parts of the system and complete the system topology by hand. I know, this sounds like a lot of manual tweaking, but this is the paradigm. Good luck! Alex MC I run a graphene nanolayer, usin the below description (from previous mail. MC Now i got an other error. It look like there is a conflict in a force MC field system, someone can suggest me how to modify it? MC the force field file came from Minoia advices, reported in the web side! MC / MC //Program grompp, VERSION 4.6.7// MC //Source code file: MC /home/marcello/DATI/software/gromacs-4.6.7/src/kernel/topio.c, line: 752// MC // MC //Fatal error:// MC //Syntax error - File forcefield.itp, line 31// MC //Last line read:// MC //'1 3 yes 0.5 0.5'// MC //Found a second defaults directive./* MC * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcello Cammarata, Ph.D. 3208790796 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] help on Graphene Nano Sheets
Andrea Minoia's tutorial describes the setup of angles, which in the case of graphene, is extremely simple from the geometry standpoint. There is no need for chancing, just add the proper entries under [dihedraltypes] in ffbonded.itp, x2top will take care of the rest. It's also a pretty good idea to actually read the manual on the definition of angles and dihedrals. Energy minimization destroys the sheet, because there's a mess in your setup. Alex MC Hi people, MC I was able to run the graphene layer sheet, by follow your advices. MC I had a problem with the dihetral angle, MC i solved it by chancing, im the top file the funct parameter from 1 to MC 3, as reported in bold below, MC . MC [ dihedrals ] MC ; aiajakal functc0c1 c2 MC c3c4c5 MC 6 1 2 3 *3 * MC 2 1 6 5 *3 * MC 2 18887 *3* MC 1 2 3 4 *3 * MC ... MC and also, by changing in rtp files all_dihedrals from 1 to 0, MC .. MC [ bondedtypes ] MC ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih MC 1 1 3 1 *0* 3 1 0 MC .. MC But, when i run the mdrun file, after the minimizzation, the model MC result destroyer, all the atom of graphene are spreads arround monitor, MC and they are not yet connected as in the original geometry. MC I would like to have some advices. What is wrong? how i have to set the MC dihedral angles? MC Thanks. MC Il 23/04/2015 20:04, abhijit Kayal ha scritto: Hi Mercelo Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C 612.01100 0.000 A3.4e-01 3.61200e-01 Then in atomname2type.n2t file add the following lines. Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Then use g_x2top. This will work. On Thu, Apr 23, 2015 at 10:54 PM, Alex nedoma...@gmail.com wrote: I think we've covered this when I was having the same issue. If you're trying to simulate a multi-molecule system, then just copy the entire forcefield .ff folder to your local directory and modify the following files: ffbonded.itp ffnonbonded.itp atomnames2types.n2t No need to create rtp entries for graphene/nanotubes, so you can ignore that part of Andrea's tutorial. Instead of just C in his tutorial, come up with a unique label to avoid conflicts, which should then also be used in your PDB. Then what I would do is create a topology entry for just graphene and convert it to a stand-alone itp by stripping off system definitions. This is basically opening the top file, removing those definitions and resaving as *.itp. After that, you can just use pdb2gmx on the remaining parts of the system and complete the system topology by hand. I know, this sounds like a lot of manual tweaking, but this is the paradigm. Good luck! Alex MC I run a graphene nanolayer, usin the below description (from previous mail. MC Now i got an other error. It look like there is a conflict in a force MC field system, someone can suggest me how to modify it? MC the force field file came from Minoia advices, reported in the web side! MC / MC //Program grompp, VERSION 4.6.7// MC //Source code file: MC /home/marcello/DATI/software/gromacs-4.6.7/src/kernel/topio.c, line: 752// MC // MC //Fatal error:// MC //Syntax error - File forcefield.itp, line 31// MC //Last line read:// MC //'1 3 yes 0.5 0.5'// MC //Found a second defaults directive./* MC * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. MC -- MC Marcello Cammarata, Ph.D. MC 3208790796 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] help on Graphene Nano Sheets
I run a graphene nanolayer, usin the below description (from previous mail. Now i got an other error. It look like there is a conflict in a force field system, someone can suggest me how to modify it? the force field file came from Minoia advices, reported in the web side! / //Program grompp, VERSION 4.6.7// //Source code file: /home/marcello/DATI/software/gromacs-4.6.7/src/kernel/topio.c, line: 752// // //Fatal error:// //Syntax error - File forcefield.itp, line 31// //Last line read:// //'1 3 yes 0.5 0.5'// //Found a second defaults directive./* * Thanks Il 23/04/2015 14:35, Marcello Cammarata ha scritto: i unistalled GRO 5 and installed GRO4.6.7_ i run the x2top and i got this message:/ //Opening force field file /usr/local/gromacs/share/gromacs/top/cnt_oplsaa.ff/atomname2type.n2t// //There are 32 name to type translations in file cnt_oplsaa.ff// //Generating bonds from distances...// //atom 112// //There are 1 different atom types in your sample// //Generating angles and dihedrals from bonds...// //Before cleaning: 672 pairs// //Before cleaning: 672 dihedrals// //There are 168 proper dihedrals,0 impropers, 336 angles// // 504 pairs, 168 bonds and 112 atoms// //Total charge is 0, total mass is 1345.23// // //WARNING: topologies generated by g_x2top can not be trusted at face value.// // Please verify atomtypes and charges by comparison to other// // topologies/*.* I am enough happy because it now work. (i have just to reset the polymer residue that i had defined in GRO5). But i got a warning, how i can correct this warning. I don't know the type of error! Il 23/04/2015 13:50, Justin Lemkul ha scritto: On 4/23/15 4:24 AM, Marcello Cammarata wrote: Thanks Justin, and thanks Alex. If i have run the command x2top using pbd file but i got the same error. which files have i substitute to my version ( Gro5.0) with the ones from the pre-5 version? The command is the same; if you're getting a seg fault in 5.0.4 you need to use version 4.6.7. -Justin Alex did you change something in your version? i am in ubuntu OS. /GROMACS: gmx x2top, VERSION 5.0.4// //Executable: /usr/local/gromacs/bin/gmx// //Library dir: /usr/local/gromacs/share/gromacs/top// //Command line:// // g_x2top -f Graphene15x15.pdb -o cnt.top -ff cnt2_oplsaa// // //WARNING: all CONECT records are ignored// //Opening force field file /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t// //Opening force field file /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t// //There are 12 name to type translations in file cnt2_oplsaa.ff// //Generating bonds from distances...// //atom 112// //There are 1 different atom types in your sample// //Generating angles and dihedrals from bonds...// //segmentation fauld (core dump created)/ if i want run the pdb file what command need i use? the same x2top? could it work? Il 23/04/2015 01:28, Alex ha scritto: Justin, everything works for me with graphene/x2top under the latest version. Am I doing something wrong? :) On Wed, Apr 22, 2015 at 5:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/22/15 7:22 PM, marcello cammarata wrote: yes, i used the Minoia tutorial, i use a cnt_oplsaa at the first attempt, and forward i copied and modify the standard oplsaa folder. with both of them i have the same trouble. The seg fault will always occur with version 5.0.4; there is a bug we discovered a few weeks back: http://redmine.gromacs.org/issues/1711 You'll need to use an older version (pre-5.0) for x2top to work properly (or patch the code and upload a fix to solve the bug :). The inizial graphene layer was created using*VMD modelling toolbox*, that was a .pdb file, i convert it in .gro file using *editconf *command. i open the gro file using Avogadro, and it is still a layer. But in the gro file the connections are loose. CONECT entries in PDB files are rarely (never?) used in GROMACS. They are totally irrelevant for the purpose of x2top. -Justin here i report the firt 5 rows of the graphene.gro file. UNNAMED 112 1GRA C1 0.000 0.000 0.000 2GRA C2 -0.123 0.071 0.000 3GRA C3 -0.123 0.213 0.000 4GRA C4 0.000 0.284 0.000 5GRA C5 0.246 0.000 0.000 thanks Il 22/04/2015 19:46, Alex ha scritto: Hello, The forcefields for CNT and graphene are identical (for the purpose of this discussion). Two questions: 1. Where did you get the initial graphene structure? 2. Are there any CONECT statements in it? I assume you used Andrea Minoia's guide and the contents of your cnt2_oplsaa.ff directory correspond to what he's got. Alex MC Hi, MC i am trying to model a Graphene nano sheet GNS on Gromacs- MC I follow the advices about the nanotubes presented in the help site. MC
Re: [gmx-users] help on Graphene Nano Sheets
Hi Mercelo Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C 612.01100 0.000 A3.4e-01 3.61200e-01 Then in atomname2type.n2t file add the following lines. Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Then use g_x2top. This will work. On Thu, Apr 23, 2015 at 10:54 PM, Alex nedoma...@gmail.com wrote: I think we've covered this when I was having the same issue. If you're trying to simulate a multi-molecule system, then just copy the entire forcefield .ff folder to your local directory and modify the following files: ffbonded.itp ffnonbonded.itp atomnames2types.n2t No need to create rtp entries for graphene/nanotubes, so you can ignore that part of Andrea's tutorial. Instead of just C in his tutorial, come up with a unique label to avoid conflicts, which should then also be used in your PDB. Then what I would do is create a topology entry for just graphene and convert it to a stand-alone itp by stripping off system definitions. This is basically opening the top file, removing those definitions and resaving as *.itp. After that, you can just use pdb2gmx on the remaining parts of the system and complete the system topology by hand. I know, this sounds like a lot of manual tweaking, but this is the paradigm. Good luck! Alex MC I run a graphene nanolayer, usin the below description (from previous mail. MC Now i got an other error. It look like there is a conflict in a force MC field system, someone can suggest me how to modify it? MC the force field file came from Minoia advices, reported in the web side! MC / MC //Program grompp, VERSION 4.6.7// MC //Source code file: MC /home/marcello/DATI/software/gromacs-4.6.7/src/kernel/topio.c, line: 752// MC // MC //Fatal error:// MC //Syntax error - File forcefield.itp, line 31// MC //Last line read:// MC //'1 3 yes 0.5 0.5'// MC //Found a second defaults directive./* MC * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] help on Graphene Nano Sheets
I think we've covered this when I was having the same issue. If you're trying to simulate a multi-molecule system, then just copy the entire forcefield .ff folder to your local directory and modify the following files: ffbonded.itp ffnonbonded.itp atomnames2types.n2t No need to create rtp entries for graphene/nanotubes, so you can ignore that part of Andrea's tutorial. Instead of just C in his tutorial, come up with a unique label to avoid conflicts, which should then also be used in your PDB. Then what I would do is create a topology entry for just graphene and convert it to a stand-alone itp by stripping off system definitions. This is basically opening the top file, removing those definitions and resaving as *.itp. After that, you can just use pdb2gmx on the remaining parts of the system and complete the system topology by hand. I know, this sounds like a lot of manual tweaking, but this is the paradigm. Good luck! Alex MC I run a graphene nanolayer, usin the below description (from previous mail. MC Now i got an other error. It look like there is a conflict in a force MC field system, someone can suggest me how to modify it? MC the force field file came from Minoia advices, reported in the web side! MC / MC //Program grompp, VERSION 4.6.7// MC //Source code file: MC /home/marcello/DATI/software/gromacs-4.6.7/src/kernel/topio.c, line: 752// MC // MC //Fatal error:// MC //Syntax error - File forcefield.itp, line 31// MC //Last line read:// MC //'1 3 yes 0.5 0.5'// MC //Found a second defaults directive./* MC * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] help on Graphene Nano Sheets
Thanks Justin, and thanks Alex. If i have run the command x2top using pbd file but i got the same error. which files have i substitute to my version ( Gro5.0) with the ones from the pre-5 version? Alex did you change something in your version? i am in ubuntu OS. /GROMACS: gmx x2top, VERSION 5.0.4// //Executable: /usr/local/gromacs/bin/gmx// //Library dir: /usr/local/gromacs/share/gromacs/top// //Command line:// // g_x2top -f Graphene15x15.pdb -o cnt.top -ff cnt2_oplsaa// // //WARNING: all CONECT records are ignored// //Opening force field file /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t// //Opening force field file /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t// //There are 12 name to type translations in file cnt2_oplsaa.ff// //Generating bonds from distances...// //atom 112// //There are 1 different atom types in your sample// //Generating angles and dihedrals from bonds...// //segmentation fauld (core dump created)/ if i want run the pdb file what command need i use? the same x2top? could it work? Il 23/04/2015 01:28, Alex ha scritto: Justin, everything works for me with graphene/x2top under the latest version. Am I doing something wrong? :) On Wed, Apr 22, 2015 at 5:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/22/15 7:22 PM, marcello cammarata wrote: yes, i used the Minoia tutorial, i use a cnt_oplsaa at the first attempt, and forward i copied and modify the standard oplsaa folder. with both of them i have the same trouble. The seg fault will always occur with version 5.0.4; there is a bug we discovered a few weeks back: http://redmine.gromacs.org/issues/1711 You'll need to use an older version (pre-5.0) for x2top to work properly (or patch the code and upload a fix to solve the bug :). The inizial graphene layer was created using*VMD modelling toolbox*, that was a .pdb file, i convert it in .gro file using *editconf *command. i open the gro file using Avogadro, and it is still a layer. But in the gro file the connections are loose. CONECT entries in PDB files are rarely (never?) used in GROMACS. They are totally irrelevant for the purpose of x2top. -Justin here i report the firt 5 rows of the graphene.gro file. UNNAMED 112 1GRA C1 0.000 0.000 0.000 2GRA C2 -0.123 0.071 0.000 3GRA C3 -0.123 0.213 0.000 4GRA C4 0.000 0.284 0.000 5GRA C5 0.246 0.000 0.000 thanks Il 22/04/2015 19:46, Alex ha scritto: Hello, The forcefields for CNT and graphene are identical (for the purpose of this discussion). Two questions: 1. Where did you get the initial graphene structure? 2. Are there any CONECT statements in it? I assume you used Andrea Minoia's guide and the contents of your cnt2_oplsaa.ff directory correspond to what he's got. Alex MC Hi, MC i am trying to model a Graphene nano sheet GNS on Gromacs- MC I follow the advices about the nanotubes presented in the help site. MC _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_ MC I run this command to greate the topology: MC _g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_ MC I got this error message: MC GROMACS: gmx x2top, VERSION 5.0.4 MC Executable: /usr/local/gromacs/bin/gmx MC Library dir: /usr/local/gromacs/share/gromacs/top MC Command line: MCg_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t MC There are 12 name to type translations in file cnt2_oplsaa.ff MC Generating bonds from distances... MC atom 112 MC There are 1 different atom types in your sample MC Generating angles and dihedrals from bonds... MC segmentazion fault (core dump created) MC Someone can help me on this? MC The graphene force field for nanolayer is the same for nanotube? There MC is something that i have to change? MC bests MC -- MC Marcello Cammarata, Ph.D. MC 3208790796 -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcello Cammarata, Ph.D. 3208790796 -- Gromacs Users mailing list * Please
Re: [gmx-users] help on Graphene Nano Sheets
On 4/23/15 4:24 AM, Marcello Cammarata wrote: Thanks Justin, and thanks Alex. If i have run the command x2top using pbd file but i got the same error. which files have i substitute to my version ( Gro5.0) with the ones from the pre-5 version? The command is the same; if you're getting a seg fault in 5.0.4 you need to use version 4.6.7. -Justin Alex did you change something in your version? i am in ubuntu OS. /GROMACS: gmx x2top, VERSION 5.0.4// //Executable: /usr/local/gromacs/bin/gmx// //Library dir: /usr/local/gromacs/share/gromacs/top// //Command line:// // g_x2top -f Graphene15x15.pdb -o cnt.top -ff cnt2_oplsaa// // //WARNING: all CONECT records are ignored// //Opening force field file /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t// //Opening force field file /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t// //There are 12 name to type translations in file cnt2_oplsaa.ff// //Generating bonds from distances...// //atom 112// //There are 1 different atom types in your sample// //Generating angles and dihedrals from bonds...// //segmentation fauld (core dump created)/ if i want run the pdb file what command need i use? the same x2top? could it work? Il 23/04/2015 01:28, Alex ha scritto: Justin, everything works for me with graphene/x2top under the latest version. Am I doing something wrong? :) On Wed, Apr 22, 2015 at 5:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/22/15 7:22 PM, marcello cammarata wrote: yes, i used the Minoia tutorial, i use a cnt_oplsaa at the first attempt, and forward i copied and modify the standard oplsaa folder. with both of them i have the same trouble. The seg fault will always occur with version 5.0.4; there is a bug we discovered a few weeks back: http://redmine.gromacs.org/issues/1711 You'll need to use an older version (pre-5.0) for x2top to work properly (or patch the code and upload a fix to solve the bug :). The inizial graphene layer was created using*VMD modelling toolbox*, that was a .pdb file, i convert it in .gro file using *editconf *command. i open the gro file using Avogadro, and it is still a layer. But in the gro file the connections are loose. CONECT entries in PDB files are rarely (never?) used in GROMACS. They are totally irrelevant for the purpose of x2top. -Justin here i report the firt 5 rows of the graphene.gro file. UNNAMED 112 1GRA C1 0.000 0.000 0.000 2GRA C2 -0.123 0.071 0.000 3GRA C3 -0.123 0.213 0.000 4GRA C4 0.000 0.284 0.000 5GRA C5 0.246 0.000 0.000 thanks Il 22/04/2015 19:46, Alex ha scritto: Hello, The forcefields for CNT and graphene are identical (for the purpose of this discussion). Two questions: 1. Where did you get the initial graphene structure? 2. Are there any CONECT statements in it? I assume you used Andrea Minoia's guide and the contents of your cnt2_oplsaa.ff directory correspond to what he's got. Alex MC Hi, MC i am trying to model a Graphene nano sheet GNS on Gromacs- MC I follow the advices about the nanotubes presented in the help site. MC _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_ MC I run this command to greate the topology: MC _g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_ MC I got this error message: MC GROMACS: gmx x2top, VERSION 5.0.4 MC Executable: /usr/local/gromacs/bin/gmx MC Library dir: /usr/local/gromacs/share/gromacs/top MC Command line: MCg_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t MC There are 12 name to type translations in file cnt2_oplsaa.ff MC Generating bonds from distances... MC atom 112 MC There are 1 different atom types in your sample MC Generating angles and dihedrals from bonds... MC segmentazion fault (core dump created) MC Someone can help me on this? MC The graphene force field for nanolayer is the same for nanotube? There MC is something that i have to change? MC bests MC -- MC Marcello Cammarata, Ph.D. MC 3208790796 -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit
[gmx-users] help on Graphene Nano Sheets
Hi, i am trying to model a Graphene nano sheet GNS on Gromacs- I follow the advices about the nanotubes presented in the help site. _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_ I run this command to greate the topology: _g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_ I got this error message: GROMACS: gmx x2top, VERSION 5.0.4 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa Opening force field file /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t Opening force field file /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t There are 12 name to type translations in file cnt2_oplsaa.ff Generating bonds from distances... atom 112 There are 1 different atom types in your sample Generating angles and dihedrals from bonds... segmentazion fault (core dump created) Someone can help me on this? The graphene force field for nanolayer is the same for nanotube? There is something that i have to change? bests -- Marcello Cammarata, Ph.D. 3208790796 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] help on Graphene Nano Sheets
Hello, The forcefields for CNT and graphene are identical (for the purpose of this discussion). Two questions: 1. Where did you get the initial graphene structure? 2. Are there any CONECT statements in it? I assume you used Andrea Minoia's guide and the contents of your cnt2_oplsaa.ff directory correspond to what he's got. Alex MC Hi, MC i am trying to model a Graphene nano sheet GNS on Gromacs- MC I follow the advices about the nanotubes presented in the help site. MC _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_ MC I run this command to greate the topology: MC _g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_ MC I got this error message: MC GROMACS: gmx x2top, VERSION 5.0.4 MC Executable: /usr/local/gromacs/bin/gmx MC Library dir: /usr/local/gromacs/share/gromacs/top MC Command line: MCg_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t MC There are 12 name to type translations in file cnt2_oplsaa.ff MC Generating bonds from distances... MC atom 112 MC There are 1 different atom types in your sample MC Generating angles and dihedrals from bonds... MC segmentazion fault (core dump created) MC Someone can help me on this? MC The graphene force field for nanolayer is the same for nanotube? There MC is something that i have to change? MC bests MC -- MC Marcello Cammarata, Ph.D. MC 3208790796 -- Best regards, Alexmailto:nedoma...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] help on Graphene Nano Sheets
Justin, everything works for me with graphene/x2top under the latest version. Am I doing something wrong? :) On Wed, Apr 22, 2015 at 5:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/22/15 7:22 PM, marcello cammarata wrote: yes, i used the Minoia tutorial, i use a cnt_oplsaa at the first attempt, and forward i copied and modify the standard oplsaa folder. with both of them i have the same trouble. The seg fault will always occur with version 5.0.4; there is a bug we discovered a few weeks back: http://redmine.gromacs.org/issues/1711 You'll need to use an older version (pre-5.0) for x2top to work properly (or patch the code and upload a fix to solve the bug :). The inizial graphene layer was created using*VMD modelling toolbox*, that was a .pdb file, i convert it in .gro file using *editconf *command. i open the gro file using Avogadro, and it is still a layer. But in the gro file the connections are loose. CONECT entries in PDB files are rarely (never?) used in GROMACS. They are totally irrelevant for the purpose of x2top. -Justin here i report the firt 5 rows of the graphene.gro file. UNNAMED 112 1GRA C1 0.000 0.000 0.000 2GRA C2 -0.123 0.071 0.000 3GRA C3 -0.123 0.213 0.000 4GRA C4 0.000 0.284 0.000 5GRA C5 0.246 0.000 0.000 thanks Il 22/04/2015 19:46, Alex ha scritto: Hello, The forcefields for CNT and graphene are identical (for the purpose of this discussion). Two questions: 1. Where did you get the initial graphene structure? 2. Are there any CONECT statements in it? I assume you used Andrea Minoia's guide and the contents of your cnt2_oplsaa.ff directory correspond to what he's got. Alex MC Hi, MC i am trying to model a Graphene nano sheet GNS on Gromacs- MC I follow the advices about the nanotubes presented in the help site. MC _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_ MC I run this command to greate the topology: MC _g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_ MC I got this error message: MC GROMACS: gmx x2top, VERSION 5.0.4 MC Executable: /usr/local/gromacs/bin/gmx MC Library dir: /usr/local/gromacs/share/gromacs/top MC Command line: MCg_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t MC There are 12 name to type translations in file cnt2_oplsaa.ff MC Generating bonds from distances... MC atom 112 MC There are 1 different atom types in your sample MC Generating angles and dihedrals from bonds... MC segmentazion fault (core dump created) MC Someone can help me on this? MC The graphene force field for nanolayer is the same for nanotube? There MC is something that i have to change? MC bests MC -- MC Marcello Cammarata, Ph.D. MC 3208790796 -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] help on Graphene Nano Sheets
On 4/22/15 7:22 PM, marcello cammarata wrote: yes, i used the Minoia tutorial, i use a cnt_oplsaa at the first attempt, and forward i copied and modify the standard oplsaa folder. with both of them i have the same trouble. The seg fault will always occur with version 5.0.4; there is a bug we discovered a few weeks back: http://redmine.gromacs.org/issues/1711 You'll need to use an older version (pre-5.0) for x2top to work properly (or patch the code and upload a fix to solve the bug :). The inizial graphene layer was created using*VMD modelling toolbox*, that was a .pdb file, i convert it in .gro file using *editconf *command. i open the gro file using Avogadro, and it is still a layer. But in the gro file the connections are loose. CONECT entries in PDB files are rarely (never?) used in GROMACS. They are totally irrelevant for the purpose of x2top. -Justin here i report the firt 5 rows of the graphene.gro file. UNNAMED 112 1GRA C1 0.000 0.000 0.000 2GRA C2 -0.123 0.071 0.000 3GRA C3 -0.123 0.213 0.000 4GRA C4 0.000 0.284 0.000 5GRA C5 0.246 0.000 0.000 thanks Il 22/04/2015 19:46, Alex ha scritto: Hello, The forcefields for CNT and graphene are identical (for the purpose of this discussion). Two questions: 1. Where did you get the initial graphene structure? 2. Are there any CONECT statements in it? I assume you used Andrea Minoia's guide and the contents of your cnt2_oplsaa.ff directory correspond to what he's got. Alex MC Hi, MC i am trying to model a Graphene nano sheet GNS on Gromacs- MC I follow the advices about the nanotubes presented in the help site. MC _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_ MC I run this command to greate the topology: MC _g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_ MC I got this error message: MC GROMACS: gmx x2top, VERSION 5.0.4 MC Executable: /usr/local/gromacs/bin/gmx MC Library dir: /usr/local/gromacs/share/gromacs/top MC Command line: MCg_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t MC There are 12 name to type translations in file cnt2_oplsaa.ff MC Generating bonds from distances... MC atom 112 MC There are 1 different atom types in your sample MC Generating angles and dihedrals from bonds... MC segmentazion fault (core dump created) MC Someone can help me on this? MC The graphene force field for nanolayer is the same for nanotube? There MC is something that i have to change? MC bests MC -- MC Marcello Cammarata, Ph.D. MC 3208790796 -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] help on Graphene Nano Sheets
yes, i used the Minoia tutorial, i use a cnt_oplsaa at the first attempt, and forward i copied and modify the standard oplsaa folder. with both of them i have the same trouble. The inizial graphene layer was created using*VMD modelling toolbox*, that was a .pdb file, i convert it in .gro file using *editconf *command. i open the gro file using Avogadro, and it is still a layer. But in the gro file the connections are loose. here i report the firt 5 rows of the graphene.gro file. UNNAMED 112 1GRA C1 0.000 0.000 0.000 2GRA C2 -0.123 0.071 0.000 3GRA C3 -0.123 0.213 0.000 4GRA C4 0.000 0.284 0.000 5GRA C5 0.246 0.000 0.000 thanks Il 22/04/2015 19:46, Alex ha scritto: Hello, The forcefields for CNT and graphene are identical (for the purpose of this discussion). Two questions: 1. Where did you get the initial graphene structure? 2. Are there any CONECT statements in it? I assume you used Andrea Minoia's guide and the contents of your cnt2_oplsaa.ff directory correspond to what he's got. Alex MC Hi, MC i am trying to model a Graphene nano sheet GNS on Gromacs- MC I follow the advices about the nanotubes presented in the help site. MC _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_ MC I run this command to greate the topology: MC _g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_ MC I got this error message: MC GROMACS: gmx x2top, VERSION 5.0.4 MC Executable: /usr/local/gromacs/bin/gmx MC Library dir: /usr/local/gromacs/share/gromacs/top MC Command line: MCg_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t MC There are 12 name to type translations in file cnt2_oplsaa.ff MC Generating bonds from distances... MC atom 112 MC There are 1 different atom types in your sample MC Generating angles and dihedrals from bonds... MC segmentazion fault (core dump created) MC Someone can help me on this? MC The graphene force field for nanolayer is the same for nanotube? There MC is something that i have to change? MC bests MC -- MC Marcello Cammarata, Ph.D. MC 3208790796 -- Marcello Cammarata, Ph.D. 3208790796 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] help on Graphene Nano Sheets
You don't need to run x2top on the GRO file, you can apply it directly to the PDB. It seems like the PDB to GRO conversion destroyed the coordinates due to poor formatting of the initial coordinates. This has nothing to do with the forcefields or graphene, you may just have a crappy PDB. Alex On Wed, Apr 22, 2015 at 5:22 PM, marcello cammarata marcello.cammar...@unipa.it wrote: yes, i used the Minoia tutorial, i use a cnt_oplsaa at the first attempt, and forward i copied and modify the standard oplsaa folder. with both of them i have the same trouble. The inizial graphene layer was created using* VMD modelling toolbox*, that was a .pdb file, i convert it in .gro file using *editconf *command. i open the gro file using Avogadro, and it is still a layer. But in the gro file the connections are loose. here i report the firt 5 rows of the graphene.gro file. UNNAMED 112 1GRA C1 0.000 0.000 0.000 2GRA C2 -0.123 0.071 0.000 3GRA C3 -0.123 0.213 0.000 4GRA C4 0.000 0.284 0.000 5GRA C5 0.246 0.000 0.000 thanks Il 22/04/2015 19:46, Alex ha scritto: Hello, The forcefields for CNT and graphene are identical (for the purpose of this discussion). Two questions: 1. Where did you get the initial graphene structure? 2. Are there any CONECT statements in it? I assume you used Andrea Minoia's guide and the contents of your cnt2_oplsaa.ff directory correspond to what he's got. Alex MC Hi, MC i am trying to model a Graphene nano sheet GNS on Gromacs- MC I follow the advices about the nanotubes presented in the help site. MC _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_ MC I run this command to greate the topology: MC _g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_ MC I got this error message: MC GROMACS: gmx x2top, VERSION 5.0.4 MC Executable: /usr/local/gromacs/bin/gmx MC Library dir: /usr/local/gromacs/share/gromacs/top MC Command line: MCg_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t MC Opening force field file MC /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t MC There are 12 name to type translations in file cnt2_oplsaa.ff MC Generating bonds from distances... MC atom 112 MC There are 1 different atom types in your sample MC Generating angles and dihedrals from bonds... MC segmentazion fault (core dump created) MC Someone can help me on this? MC The graphene force field for nanolayer is the same for nanotube? There MC is something that i have to change? MC bests MC -- MC Marcello Cammarata, Ph.D. MC 3208790796 -- Marcello Cammarata, Ph.D.3208790796 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
