[gmx-users] bonded Buckingham interaction
Hi everyone, I am trying to implement a force field for a metalorganic crystal. In this FF, there is a Buckingham interaction between two neighboring atoms, O and Zn. This interaction exists only for atoms on the same crystal site. So, bonded Buckingham interaction added in [ pairs ] would be a perfect solution. But reading through the manual, it doesn't appear that bonded Buckingham is supported If this is the case (I'd love to be wrong here), what parts of code would I have to modify to make this happen (I hope this doesn't involve any major hacking)? Thanks for your help. F. P.S. I should probably mention, I tried to use nonbonded Buckingham, cutting it off beyond a single crystal site, but this doesn't seem possible. My lattice constant is about 12A, Coulomb cuttof at 10A, and it seems like there is no suitable combination of rcoulomb, rlist and rvdw that would cut off Buckingham short of neighboring site (while allowing Coulomb to reach that neighboring site). ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bonded Buckingham interaction
Frankie Montenegro wrote: Hi everyone, I am trying to implement a force field for a metalorganic crystal. In this FF, there is a Buckingham interaction between two neighboring atoms, O and Zn. This interaction exists only for atoms on the same crystal site. How about using a Morse potential? It is quite similar. Alt. you can modify the Morse potential. So, bonded Buckingham interaction added in [ pairs ] would be a perfect solution. But reading through the manual, it doesn't appear that bonded Buckingham is supported If this is the case (I'd love to be wrong here), what parts of code would I have to modify to make this happen (I hope this doesn't involve any major hacking)? Thanks for your help. F. P.S. I should probably mention, I tried to use nonbonded Buckingham, cutting it off beyond a single crystal site, but this doesn't seem possible. My lattice constant is about 12A, Coulomb cuttof at 10A, and it seems like there is no suitable combination of rcoulomb, rlist and rvdw that would cut off Buckingham short of neighboring site (while allowing Coulomb to reach that neighboring site). ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bonded Buckingham interaction
Well, that's not an option, I am using a modified Morse interaction already. That was straightforward, I only needed to modify bondfree.c But I saw in the manual (after sending the first email) the list of files that need to be modified to add a bonded interaction, so I'll try that. BTW, it would be much easier to use nonbonded Buckingham: is there no way I could set up rvdw at 5A while keeping rcoulomb at 10A? Thanks, F. On Nov 9, 2007 4:14 AM, David van der Spoel [EMAIL PROTECTED] wrote: Frankie Montenegro wrote: Hi everyone, I am trying to implement a force field for a metalorganic crystal. In this FF, there is a Buckingham interaction between two neighboring atoms, O and Zn. This interaction exists only for atoms on the same crystal site. How about using a Morse potential? It is quite similar. Alt. you can modify the Morse potential. So, bonded Buckingham interaction added in [ pairs ] would be a perfect solution. But reading through the manual, it doesn't appear that bonded Buckingham is supported If this is the case (I'd love to be wrong here), what parts of code would I have to modify to make this happen (I hope this doesn't involve any major hacking)? Thanks for your help. F. P.S. I should probably mention, I tried to use nonbonded Buckingham, cutting it off beyond a single crystal site, but this doesn't seem possible. My lattice constant is about 12A, Coulomb cuttof at 10A, and it seems like there is no suitable combination of rcoulomb, rlist and rvdw that would cut off Buckingham short of neighboring site (while allowing Coulomb to reach that neighboring site). ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bonded Buckingham interaction
Frankie Montenegro wrote: Well, that's not an option, I am using a modified Morse interaction already. That was straightforward, I only needed to modify bondfree.c But I saw in the manual (after sending the first email) the list of files that need to be modified to add a bonded interaction, so I'll try that. BTW, it would be much easier to use nonbonded Buckingham: is there no way I could set up rvdw at 5A while keeping rcoulomb at 10A? Thanks, what makes you think you can not use Non-bonded Buckingham? We shouild have the option to have Buckingham pairs though. Please add it to the development page of the wiki. F. On Nov 9, 2007 4:14 AM, David van der Spoel [EMAIL PROTECTED] wrote: Frankie Montenegro wrote: Hi everyone, I am trying to implement a force field for a metalorganic crystal. In this FF, there is a Buckingham interaction between two neighboring atoms, O and Zn. This interaction exists only for atoms on the same crystal site. How about using a Morse potential? It is quite similar. Alt. you can modify the Morse potential. So, bonded Buckingham interaction added in [ pairs ] would be a perfect solution. But reading through the manual, it doesn't appear that bonded Buckingham is supported If this is the case (I'd love to be wrong here), what parts of code would I have to modify to make this happen (I hope this doesn't involve any major hacking)? Thanks for your help. F. P.S. I should probably mention, I tried to use nonbonded Buckingham, cutting it off beyond a single crystal site, but this doesn't seem possible. My lattice constant is about 12A, Coulomb cuttof at 10A, and it seems like there is no suitable combination of rcoulomb, rlist and rvdw that would cut off Buckingham short of neighboring site (while allowing Coulomb to reach that neighboring site). ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bonded Buckingham interaction
From: Frankie Montenegro [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] bonded Buckingham interaction Date: Fri, 9 Nov 2007 04:47:02 -0500 Well, that's not an option, I am using a modified Morse interaction already. That was straightforward, I only needed to modify bondfree.c But I saw in the manual (after sending the first email) the list of files that need to be modified to add a bonded interaction, so I'll try that. BTW, it would be much easier to use nonbonded Buckingham: is there no way I could set up rvdw at 5A while keeping rcoulomb at 10A? Thanks, F. You can always use user-defined tabulated non-bonded potentials. (see the manual) Berk. _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx 3.3.2 explodes with libc.so.6
Dear Li Qiang, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the single and double precision tests passed with and without assembly loop optimizations so I guess it's not simply Ubuntu 7.10 that is to blame (unless what you are seeing is a 32-bit distribution-specific problem?). Cheers, Bruce -- Hamewith - the road that's never dreary Dr. Bruce F. Milne CEQOFFUP Faculdade de Farmácia Universidade do Porto Rua Aníbal Cunha - 164 4050-047 Porto Portugal email: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to set N-terminal lysine carry only +1 unit charge?
Hi, I am using amber force field in Gromacs. The protein I simulated is the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be neutral. According to rules using Amber in Gromacs, neutral lysine should be named to LYN. Everything goes smoothly except the N-terminal lysine residue. It should carry +1 unit charge due to its location. According to the rules, I should rename this residue as NLYN. But I can not find NLYN in ffamber*.rtp. In other words, error will appear if I do so. I did not get response from Dear Dr. Eric J. Sorin who establish amber port into gromacs. So anyone knows how to set N-terminal lysine residue carry +1, not +2 unit charges using Amber FF in gmx? Zhongqiao National University of Singapore ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx 3.3.2 explodes with libc.so.6
Dmytro Kovalskyy wrote: Hi there, Gromacs explodes with new version of libc Did you compile it yourself? Could you please recompile it with CFLAGS=-g and try to debug it? Which OS and compilers did tou use? The story does not end here. I found that behavior of GROMACS depends on the flag CFLAGS=-g, but not on glibc version. This means that when I recompile the program with the flag everything works regardless what version of glibc I use. [EMAIL PROTECTED] ~]$ uname -a Linux violet.enamine.net 2.6.18-std-smp-alt7 #1 SMP Sat Aug 4 00:07:54 MSD 2007 i686 GNU/Linux [EMAIL PROTECTED] ~]$ rpm -qa gcc gcc4.1-4.1.1-alt11 libgcc4.1-4.1.1-alt11 gcc4.1-c++-4.1.1-alt11 gcc4.1-fortran-4.1.1-alt11 gcc-c++-common-1.4.10-alt2 gcc-fortran-common-1.4.10-alt2 gcc-common-1.4.10-alt2 Dima ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to set N-terminal lysine carry only +1 unit charge?
it could not be possible since amber force field doesn't parameterized NLYN. alternative, use ACE/NME to cap the peptide. On 11/9/2007 7:36 PM, Hu Zhongqiao wrote: Hi, I am using amber force field in Gromacs. The protein I simulated is the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be neutral. According to rules using Amber in Gromacs, neutral lysine should be named to LYN. Everything goes smoothly except the N-terminal lysine residue. It should carry +1 unit charge due to its location. According to the rules, I should rename this residue as NLYN. But I can not find NLYN in ffamber*.rtp. In other words, error will appear if I do so. I did not get response from Dear Dr. Eric J. Sorin who establish amber port into gromacs. So anyone knows how to set N-terminal lysine residue carry +1, not +2 unit charges using Amber FF in gmx? Zhongqiao National University of Singapore ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx 3.3.2 explodes with libc.so.6
I see. thanks for the information. but one of my friends nearby failed on this combination just few hours ago. Maybe we need more test for the conclusion. Li Qiang On Fri, 2007-11-09 at 10:47 +, Bruce Milne wrote: Dear Li Qiang, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the single and double precision tests passed with and without assembly loop optimizations so I guess it's not simply Ubuntu 7.10 that is to blame (unless what you are seeing is a 32-bit distribution-specific problem?). Cheers, Bruce ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx 3.3.2 explodes with libc.so.6
Yes. Mine is 32-bit. Intel P4 3.0G. On Fri, 2007-11-09 at 10:47 +, Bruce Milne wrote: Dear Li Qiang, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the single and double precision tests passed with and without assembly loop optimizations so I guess it's not simply Ubuntu 7.10 that is to blame (unless what you are seeing is a 32-bit distribution-specific problem?). Cheers, Bruce ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx 3.3.2 explodes with libc.so.6
Hi, Please be clear that failed test: simple/rb1 and complex/acetonitrilRF are due to different reasons. So far, simple/rb1 remains unknown but complex/acetonitrilRF has been solved. Also, a segmentation fault is different from results having difference to the benchmark data. Please be exact about their failure pattern when reporting. The fix of acetonitrilRF is available in the CVS. Even you don't apply, it won't affect if you are using parallel and you are not using RF. Regards, Yang Ye On 11/9/2007 7:49 PM, Li Qiang wrote: I see. thanks for the information. but one of my friends nearby failed on this combination just few hours ago. Maybe we need more test for the conclusion. Li Qiang On Fri, 2007-11-09 at 10:47 +, Bruce Milne wrote: Dear Li Qiang, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the single and double precision tests passed with and without assembly loop optimizations so I guess it's not simply Ubuntu 7.10 that is to blame (unless what you are seeing is a 32-bit distribution-specific problem?). Cheers, Bruce ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx 3.3.2 explodes with libc.so.6
On 11/9/2007 6:47 PM, Bruce Milne wrote: Dear Li Qiang, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the single and double precision tests passed with and without assembly loop optimizations so I guess it's not simply Ubuntu 7.10 that is to blame (unless what you are seeing is a 32-bit distribution-specific problem?). Quite likely a 32-bit specific problem. Could anyone install dmalloc and configure gromacs to build with dmalloc and run the test with the new mdrun? I did mine and found that it was due to one line in mshift.c srenew(g-edge[0],n); mdrun output: realloc for g-edge[0] (24 bytes, file mshift.c, line 251, g-edge[0]=0x0x 1) Regards, Yang Ye Cheers, Bruce ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] coordinate files for molecules consisting of new (non-standard) residues
Dear gromacs users, I am trying to set up a system with new (non-standard) residue blocks to study polymers and polymer-protein conjugates; however we will not have pdb files of molecules that we want to study. Is there a way of generating coordinate files and other necessary Gromacs files using only a sequence of these novel residues instead of the using pdb file and pdb2gmx? Thank you Teresa ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] installation error
Date: Thu, 8 Nov 2007 12:35:29 +1100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] installation error pragya chohan wrote: hi I had installed make_hole utility earlier but when i tried to run: make_hole.pl -f box_popc.pdb -o hole_popc.pdb -r 9.0 -lipat P8 -lipid POPC -cx 51.5 -cy 51.8 I get : bash: make_hole.pl: command not found. So make-hole.pl, or something in its shebang line is probably not in your path. I tried reinstalling it by ./configure which completed successfully but when i ran make command i get the following error: This is the output from configuring GROMACS, not make_hole.pl In any case, you should do make distclean between runs of configure with different settings, and/or system configuration. Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Thanks for your reply. when i run make distclean i get following error: make[2]: *** No rule to make target `.deps/wnblist.Plo'. Stop. make[2]: Leaving directory `/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src/mdlib' make[1]: *** [distclean-recursive] Error 1 make[1]: Leaving directory `/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src' make: *** [distclean-recursive] Error 1 _ Windows Live Spaces is here! It’s easy to create your own personal Web site. http://spaces.live.com/?mkt=en-in___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] installation error
pragya chohan wrote: Date: Thu, 8 Nov 2007 12:35:29 +1100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] installation error pragya chohan wrote: hi I had installed make_hole utility earlier but when i tried to run: make_hole.pl -f box_popc.pdb -o hole_popc.pdb -r 9.0 -lipat P8 -lipid POPC -cx 51.5 -cy 51.8 I get : bash: make_hole.pl: command not found. So make-hole.pl, or something in its shebang line is probably not in your path. I tried reinstalling it by ./configure which completed successfully but when i ran make command i get the following error: This is the output from configuring GROMACS, not make_hole.pl In any case, you should do make distclean between runs of configure with different settings, and/or system configuration. Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Pleas e search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Thanks for your reply. when i run make distclean i get following error: make[2]: *** No rule to make target `.deps/wnblist.Plo'. Stop. make[2]: Leaving directory `/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src/mdlib' make[1]: *** [distclean-recursive] Error 1 make[1]: Leaving directory `/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src' make: *** [distclean-recursive] Error 1 _ Windows Live Spaces is here! It’s easy to create your own personal Web site. http://spaces.live.com/?mkt=en-in___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php your mail is incomprehensible. please format it to be readable. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx 3.3.2 explodes with libc.so.6
On 11/9/2007 9:09 PM, David van der Spoel wrote: Yang Ye wrote: On 11/9/2007 6:47 PM, Bruce Milne wrote: Dear Li Qiang, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the single and double precision tests passed with and without assembly loop optimizations so I guess it's not simply Ubuntu 7.10 that is to blame (unless what you are seeing is a 32-bit distribution-specific problem?). Quite likely a 32-bit specific problem. Could anyone install dmalloc and configure gromacs to build with dmalloc and run the test with the new mdrun? I did mine and found that it was due to one line in mshift.c srenew(g-edge[0],n); mdrun output: realloc for g-edge[0] (24 bytes, file mshift.c, line 251, g-edge[0]=0x0x 1) So is this in the rb1 test? I compiled the code with dmalloc on my Mac and it passed all tests (except dec+water due to very small energy differences). Yes. Try 32-bit? 64-bit on my Opteron is alright too (with and without dmalloc). Regards, Yang Ye Cheers, Bruce ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx 3.3.2 explodes with libc.so.6
Yang Ye wrote: On 11/9/2007 9:09 PM, David van der Spoel wrote: Yang Ye wrote: On 11/9/2007 6:47 PM, Bruce Milne wrote: Dear Li Qiang, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the single and double precision tests passed with and without assembly loop optimizations so I guess it's not simply Ubuntu 7.10 that is to blame (unless what you are seeing is a 32-bit distribution-specific problem?). Quite likely a 32-bit specific problem. Could anyone install dmalloc and configure gromacs to build with dmalloc and run the test with the new mdrun? I did mine and found that it was due to one line in mshift.c srenew(g-edge[0],n); mdrun output: realloc for g-edge[0] (24 bytes, file mshift.c, line 251, g-edge[0]=0x0x 1) So is this in the rb1 test? I compiled the code with dmalloc on my Mac and it passed all tests (except dec+water due to very small energy differences). Yes. Try 32-bit? 64-bit on my Opteron is alright too (with and without dmalloc). This is a 32 bit OS AFAIK (Mac OS X 10.5) with gcc 4.0.1 Anyway how did you obtain the above result? What command line? Regards, Yang Ye Cheers, Bruce ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx 3.3.2 explodes with libc.so.6
Yang Ye wrote: On 11/9/2007 6:47 PM, Bruce Milne wrote: Dear Li Qiang, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the single and double precision tests passed with and without assembly loop optimizations so I guess it's not simply Ubuntu 7.10 that is to blame (unless what you are seeing is a 32-bit distribution-specific problem?). Quite likely a 32-bit specific problem. Could anyone install dmalloc and configure gromacs to build with dmalloc and run the test with the new mdrun? I did mine and found that it was due to one line in mshift.c srenew(g-edge[0],n); mdrun output: realloc for g-edge[0] (24 bytes, file mshift.c, line 251, g-edge[0]=0x0x 1) So is this in the rb1 test? I compiled the code with dmalloc on my Mac and it passed all tests (except dec+water due to very small energy differences). Regards, Yang Ye Cheers, Bruce ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdrun error
hi i am trying to run mdrun for protein in membrane system. When i run mdrun i get a warning Step -2, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 2.144082 (between atoms 12433 and 12434) rms 0.216090 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 11761 11762 90.00.1633 0.2387 0.1000 11929 11930 31.70.1633 0.1000 0.1000 12097 12098 90.00.1632 0.1041 0.1000 12265 12266 90.00.1633 0.2266 0.1000 12433 12434 90.00.1633 0.3144 0.1000 starting mdrun 'alamethicin in popc' 500 steps, 0.5 ps. Warning: 1-4 interaction between 115 and 136 at distance 1.144 which is larger t han the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 12007 and 12008) rms inf bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 11619 11620 90.00.1000 0.1411 0.1000 11633 11634 90.00.1000 13155507200. 0.1000 11640 11641 90.00.1000 0.1214 0.1000 . 12619 12620 90.00.1080 0.1447 0.1080 Wrote pdb files with previous and current coordinates step 0Segmentation fault I am using shake in my mdp file. I want to restrain water. my mdp file is: title= popc128a integrator = md define = -DFLEX_SPC dt = 0.001 nsteps = 500 nstxout = 500 ns_type = grid pbc = xyz constraints = hbonds constraints_algorithm= shake coulombtype = PME vdwtype = cut-off rcoloumb = 1.0 nstlist = 10.0 Tcoupl = no pcoupl = no compressibility = 4.5e-5 gen_temp = 300 gen_vel = no Please help. Thanks in advance. _ Check out some new online services at Windows Live Ideas—so new they haven’t even been officially released yet. http://www.msnspecials.in/windowslive/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: How to set N-terminal lysine carry only +1 unit charge?
Thanks, Yang Ye. You mean that I put an additional ACE or NME on the N-terminal lysine residue? zhongqiao Message: 3 Date: Fri, 09 Nov 2007 20:03:21 +0800 From: Yang Ye [EMAIL PROTECTED] Subject: Re: [gmx-users] How to set N-terminal lysine carry only +1 unitcharge? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed it could not be possible since amber force field doesn't parameterized NLYN. alternative, use ACE/NME to cap the peptide. On 11/9/2007 7:36 PM, Hu Zhongqiao wrote: Hi, I am using amber force field in Gromacs. The protein I simulated is the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be neutral. According to rules using Amber in Gromacs, neutral lysine should be named to LYN. Everything goes smoothly except the N-terminal lysine residue. It should carry +1 unit charge due to its location. According to the rules, I should rename this residue as NLYN. But I can not find NLYN in ffamber*.rtp. In other words, error will appear if I do so. I did not get response from Dear Dr. Eric J. Sorin who establish amber port into gromacs. So anyone knows how to set N-terminal lysine residue carry +1, not +2 unit charges using Amber FF in gmx? Zhongqiao National University of Singapore ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun error
Check out the wiki at: http://wiki.gromacs.org/index.php/Errors#LINCS_warnings Alternatively, search the list for some of my posts from around a year ago - NVT and minimization of a lipid bilayer (or search for my name, they should come up as well). I suspect you have bad contacts in your starting structure. -Justin Quoting pragya chohan [EMAIL PROTECTED]: hi i am trying to run mdrun for protein in membrane system. When i run mdrun i get a warning Step -2, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 2.144082 (between atoms 12433 and 12434) rms 0.216090 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 11761 11762 90.00.1633 0.2387 0.1000 11929 11930 31.70.1633 0.1000 0.1000 12097 12098 90.00.1632 0.1041 0.1000 12265 12266 90.00.1633 0.2266 0.1000 12433 12434 90.00.1633 0.3144 0.1000 starting mdrun 'alamethicin in popc' 500 steps, 0.5 ps. Warning: 1-4 interaction between 115 and 136 at distance 1.144 which is larger t han the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 12007 and 12008) rms inf bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 11619 11620 90.00.1000 0.1411 0.1000 11633 11634 90.00.1000 13155507200. 0.1000 11640 11641 90.00.1000 0.1214 0.1000 . 12619 12620 90.00.1080 0.1447 0.1080 Wrote pdb files with previous and current coordinates step 0Segmentation fault I am using shake in my mdp file. I want to restrain water. my mdp file is: title= popc128a integrator = md define = -DFLEX_SPC dt = 0.001 nsteps = 500 nstxout = 500 ns_type = grid pbc = xyz constraints = hbonds constraints_algorithm= shake coulombtype = PME vdwtype = cut-off rcoloumb = 1.0 nstlist = 10.0 Tcoupl = no pcoupl = no compressibility = 4.5e-5 gen_temp = 300 gen_vel = no Please help. Thanks in advance. _ Check out some new online services at Windows Live Ideasso new they havent even been officially released yet. http://www.msnspecials.in/windowslive/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: How to set N-terminal lysine carry only +1 unit charge?
ACE for the N-termail and NME for the C-terminal. They are neutral. You can do so with aids from PyMol... Regards, Yang Ye On 11/9/2007 9:50 PM, Hu Zhongqiao wrote: Thanks, Yang Ye. You mean that I put an additional ACE or NME on the N-terminal lysine residue? zhongqiao Message: 3 Date: Fri, 09 Nov 2007 20:03:21 +0800 From: Yang Ye [EMAIL PROTECTED] Subject: Re: [gmx-users] How to set N-terminal lysine carry only +1 unitcharge? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed it could not be possible since amber force field doesn't parameterized NLYN. alternative, use ACE/NME to cap the peptide. On 11/9/2007 7:36 PM, Hu Zhongqiao wrote: Hi, I am using amber force field in Gromacs. The protein I simulated is the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be neutral. According to rules using Amber in Gromacs, neutral lysine should be named to LYN. Everything goes smoothly except the N-terminal lysine residue. It should carry +1 unit charge due to its location. According to the rules, I should rename this residue as NLYN. But I can not find NLYN in ffamber*.rtp. In other words, error will appear if I do so. I did not get response from Dear Dr. Eric J. Sorin who establish amber port into gromacs. So anyone knows how to set N-terminal lysine residue carry +1, not +2 unit charges using Amber FF in gmx? Zhongqiao National University of Singapore ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx 3.3.2 explodes with libc.so.6
On 11/9/2007 9:21 PM, David van der Spoel wrote: Yang Ye wrote: On 11/9/2007 9:09 PM, David van der Spoel wrote: Yang Ye wrote: On 11/9/2007 6:47 PM, Bruce Milne wrote: Dear Li Qiang, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the single and double precision tests passed with and without assembly loop optimizations so I guess it's not simply Ubuntu 7.10 that is to blame (unless what you are seeing is a 32-bit distribution-specific problem?). Quite likely a 32-bit specific problem. Could anyone install dmalloc and configure gromacs to build with dmalloc and run the test with the new mdrun? I did mine and found that it was due to one line in mshift.c srenew(g-edge[0],n); mdrun output: realloc for g-edge[0] (24 bytes, file mshift.c, line 251, g-edge[0]=0x0x 1) So is this in the rb1 test? I compiled the code with dmalloc on my Mac and it passed all tests (except dec+water due to very small energy differences). Yes. Try 32-bit? 64-bit on my Opteron is alright too (with and without dmalloc). This is a 32 bit OS AFAIK (Mac OS X 10.5) with gcc 4.0.1 Anyway how did you obtain the above result? What command line? My Linux is ubuntu 32-bit on P4. If mdrun is built without dmalloc, it will report realloc error from glibc. Then I built mdrun with dmalloc, and it reports the line above (realloc for g-edge[0]...,mshift.c. line 251...) Regards, Yang Ye Cheers, Bruce ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] genernal problem in simulation
Dear users: After we get some data from GMX simulation, how can we validate them? I met many difficulties in parameters setting. ___ Kitty JI Groupe Matière Condensée et Matériaux UMR-CNRS 6626 Bat. 11A, Campus de Beaulieu Université de Rennes 1 35042 Rennes cedex FRANCE Tel. : +33 2 23 23 64 97 Fax. : +33 2 23 23 67 17 ___ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genernal problem in simulation
this is a too general question. please read the wiki first. On 11/9/2007 9:58 PM, Kitty Ji wrote: Dear users: After we get some data from GMX simulation, how can we validate them? I met many difficulties in parameters setting. ___ Kitty JI Groupe Matière Condensée et Matériaux UMR-CNRS 6626 Bat. 11A, Campus de Beaulieu Université de Rennes 1 35042 Rennes cedex FRANCE Tel. : +33 2 23 23 64 97 Fax. : +33 2 23 23 67 17 ___ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to set N-terminal lysine carry only +1 unit charge?
Hell my friend, i dont need any of this messages from all the members of this board, please help alert the board, its bored reading them all, i want to unsubscribe from the group Yang Ye [EMAIL PROTECTED] wrote: it could not be possible since amber force field doesn't parameterized NLYN. alternative, use ACE/NME to cap the peptide. On 11/9/2007 7:36 PM, Hu Zhongqiao wrote: Hi, I am using amber force field in Gromacs. The protein I simulated is the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be neutral. According to rules using Amber in Gromacs, neutral lysine should be named to LYN. Everything goes smoothly except the N-terminal lysine residue. It should carry +1 unit charge due to its location. According to the rules, I should rename this residue as NLYN. But I can not find NLYN in ffamber*.rtp. In other words, error will appear if I do so. I did not get response from Dear Dr. Eric J. Sorin who establish amber port into gromacs. So anyone knows how to set N-terminal lysine residue carry +1, not +2 unit charges using Amber FF in gmx? Zhongqiao National University of Singapore ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
I want to use replica exchange method. After obtaining all files at different temperatures, how can I load the e.g 4 separate replica files to the mdrun command? I could not find any information about it. Thank you Oz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to set N-terminal lysine carry only +1 unit charge?
DIY on the admin panel http://www.gromacs.org/index.php?option=com_wrapperItemid=83 On 11/9/2007 11:04 PM, Henry O Ify wrote: Hell my friend, i dont need any of this messages from all the members of this board, please help alert the board, its bored reading them all, i want to unsubscribe from the group */Yang Ye [EMAIL PROTECTED]/* wrote: it could not be possible since amber force field doesn't parameterized NLYN. alternative, use ACE/NME to cap the peptide. On 11/9/2007 7:36 PM, Hu Zhongqiao wrote: Hi, I am using amber force field in Gromacs. The protein I simulated is the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be neutral. According to rules using Amber in Gromacs, neutral lysine should be named to LYN. Everything goes smoothly except the N-terminal lysine residue. It should carry +1 unit charge due to its location. According to the rules, I should rename this residue as NLYN. But I can not find NLYN in ffamber*.rtp. In other words, error will appear if I do so. I did not get response from Dear Dr. Eric J. Sorin who establish amber port into gromacs. So anyone knows how to set N-terminal lysine residue carry +1, not +2 unit charges using Amber FF in gmx? Zhongqiao National University of Singapore ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
I want to use replica exchange method. After obtaining all files at different temperatures, how can I load the e.g 4 separate replica files to the mdrun command? I could not find any information about it. See mdrun -h. Please choose a meaningful subject for your emails. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun error
hi i am trying to run mdrun for protein in membrane system. When i run mdrun i get a warning Check out the wiki link Justin provided. Also read http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and make sure your setup regime is reasonable. Also, when you run grompp, pay attention to the warning messages. You'll get at least one for this .mdp file. my mdp file is: title= popc128a integrator = md define = -DFLEX_SPC dt = 0.001 nsteps = 500 nstxout = 500 ns_type = grid pbc = xyz constraints = hbonds constraints_algorithm= shake coulombtype = PME vdwtype = cut-off rcoloumb = 1.0 nstlist = 10.0 Tcoupl = no pcoupl = no compressibility = 4.5e-5 gen_temp = 300 gen_vel = no Please help. Thanks in advance. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs
I installed ffamber ports for gromacs, generated gro and topology files for a DNA structure with pdb2gmx, a box with editconf and added solvation with genbox. When I try to run grompp i obtain these errors: checking input for internal consistency... calling cpp -traditional... processing topology... Generated 2628 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2628 of the 2628 1-4 parameter combinations ERROR 0 [file gr_Nast.top, line 761]: No default Bond types ERROR 0 [file gr_Nast.top, line 3352]: No default Angle types ERROR 0 [file gr_Nast.top, line 3354]: No default Angle types It seems gromacs don't read ffamber* force field information, however i using the directive include = -I\home\jantonioms\Programs\gromacs\share\gromacs\top in *.mdp file Can anyone have an idea? Thanks for help. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] coordinate files for molecules consisting of new (non-standard) residues
Dear gromacs users, I am trying to set up a system with new (non-standard) residue blocks to study polymers and polymer-protein conjugates; however we will not have pdb files of molecules that we want to study. Jumping straight in the deep end is a recipe for frustration. Make sure you do some tutorial material, and get some practice setting up systems where you haven't needed to use self-made residue blocks (if you haven't already). You will need a thorough knowledge of Chapter 5 of the manual. Is there a way of generating coordinate files and other necessary Gromacs files using only a sequence of these novel residues instead of the using pdb file and pdb2gmx? No, there is no way within GROMACS to generate coordinates of any structure, apart from adding hydrogens, and such tweaks. The wiki is currently short of recommendations for molecule builders. Can people please suggest some? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs
I installed ffamber ports for gromacs, generated gro and topology files for a DNA structure with pdb2gmx, a box with editconf and added solvation with genbox. When I try to run grompp i obtain these errors: checking input for internal consistency... calling cpp -traditional... processing topology... Generated 2628 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2628 of the 2628 1-4 parameter combinations ERROR 0 [file gr_Nast.top, line 761]: No default Bond types ERROR 0 [file gr_Nast.top, line 3352]: No default Angle types ERROR 0 [file gr_Nast.top, line 3354]: No default Angle types It seems gromacs don't read ffamber* force field information, however i using the directive include = -I\home\jantonioms\Programs\gromacs\share\gromacs\top in *.mdp file Can anyone have an idea? I don't know if it is the cause of the problem, but backslashes are not usually interpreted as directory file separators on Unix - unlike Windows. Use forward slashes. As a first guess, I'd say that cpp is interpreting your include directive with the backslashes starting escape sequences for funky meanings, hence failing to find ffamber. That assumes you've put ffamber in that location, of course! :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs
it seems there's a problem with my compiler. I succesfully run grompp in another computer with gromacs distribution. I compare and check the two ggc version. On Nov 9, 2007 7:10 PM, Mark Abraham [EMAIL PROTECTED] wrote: I installed ffamber ports for gromacs, generated gro and topology files for a DNA structure with pdb2gmx, a box with editconf and added solvation with genbox. When I try to run grompp i obtain these errors: checking input for internal consistency... calling cpp -traditional... processing topology... Generated 2628 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2628 of the 2628 1-4 parameter combinations ERROR 0 [file gr_Nast.top, line 761]: No default Bond types ERROR 0 [file gr_Nast.top, line 3352]: No default Angle types ERROR 0 [file gr_Nast.top, line 3354]: No default Angle types It seems gromacs don't read ffamber* force field information, however i using the directive include = -I\home\jantonioms\Programs\gromacs\share\gromacs\top in *.mdp file Can anyone have an idea? I don't know if it is the cause of the problem, but backslashes are not usually interpreted as directory file separators on Unix - unlike Windows. Use forward slashes. As a first guess, I'd say that cpp is interpreting your include directive with the backslashes starting escape sequences for funky meanings, hence failing to find ffamber. That assumes you've put ffamber in that location, of course! :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] soft-core and coulomb transformation
hi,
i am pasting the xmgrace file for the both forward and reverse
transformation of charge modification for Ala-Gly mutation.
The simulations are performed in water. when you open the file with
xmgrace, you can clearly see the behaviour what i was describing in
previous mails.
bharat
#
# Grace project file
#
@version 50120
@map color 11 to (255,0,0), red
@with g0
@world -0.05, -5.45, 1.05, 4.45
@view 0.15, 0.15, 1.15, 0.85
@title charge transformation
@subtitle without soft-core potentials
@xaxis on
@xaxis label \xl\f{}
@xaxis tick on
@xaxis tick major 0.2
@xaxis tick minor ticks 1
@xaxis ticklabel on
@yaxis on
@yaxis label dG/d\xl\f{} (kJ\#{b7}mol\S-1\N\#{b7}\xl\f{}\S-1\N)
@yaxis tick on
@yaxis tick major 1
@yaxis tick minor ticks 1
@yaxis ticklabel on
@legend on
@legend 0.5, 0.8
@legend box pattern 0
@s0 type xydy
@s0 errorbar on
@s0 comment FWD/coul_fwd_dgdl
@s0 legend fwd [(Ace-Ala-Nac) -- (Ace-Gly-Nac)]
@g1 on
@g1 hidden false
@g1 type XY
@g1 stacked false
@g1 bar hgap 0.00
@g1 fixedpoint off
@g1 fixedpoint type 0
@g1 fixedpoint xy 0.00, 0.00
@g1 fixedpoint format general general
@g1 fixedpoint prec 6, 6
@with g1
@world -0.05, -4.45, 1.05, 5.45
@view 0.15, 0.15, 1.15, 0.85
@xaxes invert on
@yaxes invert on
@xaxis on
@xaxis tick on
@xaxis tick major 0.2
@xaxis tick minor ticks 1
@xaxis ticklabel place opposite
@xaxis ticklabel color 11
@yaxis on
@yaxis tick on
@yaxis tick major 1
@yaxis tick minor ticks 1
@yaxis ticklabel place opposite
@yaxis ticklabel color 11
@legend on
@legend 0.5, 0.75
@legend box pattern 0
@s0 type xydy
@s0 line color 11
@s0 errorbar on
@s0 errorbar color 11
@s0 comment REV/coul_rev_dgdl
@s0 legend rev [(Ace-Gly-Nac) -- (Ace-Ala-Nac)]
@target G0.S0
@type xydy
0.00 -2.203320 0.055352
0.05 -2.299345 0.0520252
0.10 -2.358355 0.145189
0.15 -2.318708 0.108821
0.25 -2.506092 0.055204
0.35 -2.201419 0.0590116
0.45 -2.484940 0.0969871
0.50 -2.433880 0.0532859
0.55 -2.462887 0.0775993
0.65 -2.619397 0.0606133
0.75 -2.622916 0.0757515
0.85 -2.517759 0.0644187
0.90 -2.636431 0.0590214
0.95 -2.599439 0.10389
1.00 -2.563080 0.0581629
@target G1.S0
@type xydy
0.00 4.627166 0.0879965
0.05 4.118060 0.0790556
0.10 3.916284 0.0833586
0.15 3.588531 0.0804413
0.25 2.05 0.0928452
0.35 1.823581 0.0706488
0.45 1.047328 0.0957733
0.50 0.837857 0.0728831
0.55 0.529029 0.0765816
0.65 -0.281202 0.0716938
0.75 -0.995985 0.0706986
0.85 -1.947576 0.0761678
0.90 -2.328663 0.0707552
0.95 -2.589109 0.0834396
1.00 -3.052700 0.0640444
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