[gmx-users] Updating Ubuntu
Dear all, I downloaded GMX from Ubuntu, and it was the 4.0.71 version. Does anyone know or have the possibility to update UBUNTU with the latest GMX? Cheers Sergio -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] reading tpx file version 73 with version 58 program
you have generated your em1.tpr file using a newer gromacs version, and are trying to read it with an older gromacs version. Please make sure you use the same gromacs version. Try typing which grompp to find out. On Fri, Dec 24, 2010 at 8:49 AM, shikha agarwal shikhaiiit...@gmail.comwrote: hi , Mr. justin thanx a lot for ur help! now i m able to generate system_inflated.gro. but while i m performing Run energy minimization accorning to tutorial getting this error grompp -f minim.mdp -c pope.gro -p topol_pope.top -o em1.tpr mdrun -v -s em1 -o em1 -c after_em -g emlog Fatal error: reading tpx file (em1.tpr) version 73 with version 58 program with regards: shikha IIIT-A -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] reading tpx file version 73 with version 58 program
On 24/12/2010 6:49 PM, shikha agarwal wrote: hi , Mr. justin thanx a lot for ur help! now i m able to generate system_inflated.gro. but while i m performing Run energy minimization accorning to tutorial getting this error grompp -f minim.mdp -c pope.gro -p topol_pope.top -o em1.tpr mdrun -v -s em1 -o em1 -c after_em -g emlog Fatal error: reading tpx file (em1.tpr) version 73 with version 58 program This means what it says. You can't read a new version of a file with an old version of a program, just like (say) word processors. Either manage your environment better or get rid of the old versions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
On 24/12/2010 6:45 PM, Sergio Manzetti wrote: Hi thanks, but if I use make it says make no Makefile found... Right, so configure didn't work, unlike your statement that it did work... Troubleshoot the step that failed, not things that came after it... Mark On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 23/12/2010 9:12 PM, Sergio Manzetti wrote: Dear Users, I am unable to get pass the first step of ./configure . This step works, but when typing make it says: no targets specified and no makefile found. That suggests configure did not work. Should it be like this, or is it compulsory to use cmake? cmake is not compulsory. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Updating Ubuntu
On 24/12/2010 8:20 PM, Sergio Manzetti wrote: Dear all, I downloaded GMX from Ubuntu, and it was the 4.0.71 version. Does anyone know or have the possibility to update UBUNTU with the latest GMX? If it's not in the package manager, than whoever contributed it to Ubuntu hasn't updated it, I'm afraid. You are limited to that version, or reading and following the installation instructions on the GROMACS website. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong temperature coupling to make sure every replica is at its target temperature. I guess I could do it by setting tau_t small in the Nose-hoover T coupling, but there will come the warning in Gromacs. I maxwarned the warning to proceed, and find the temperature is ok, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks a lot. The temperature coupling algorithms are discussed in the literature, when they were derived (citations in GROMACS manual) and subsequently. I suggest you do your own homework there. The use of REMD is more or less irrelevant to the trade-offs when deciding what temperature coupling scheme to use. Mark Best, Qin 2010/12/21 Qin Qiao qiaoqi...@gmail.com mailto:qiaoqi...@gmail.com Dear all, I wonder what will happen in Nose-hoover coupling when tau_t = dt * nsttcouple, while nsttcouple = nstlist. (I used -maxwarn 1 to ignore the Gromacs warning) I tried this setting, to find the temperature is OK, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks in advance. Best, Qin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Reg: Simulating large number of molecules
Hi all I want to simulate more than 1000 molecules of say octane r any alkanes in gromacs. after doing a little math i find my box dimensions for the molecules. but when i use genbox to insert multiple molecules in my local system after running some time it says cannot allocate memory but when the same command i gave it in a Linux cluster interactively (HPCE) it goes well and fills the box with required number of molecules and i get the correct density. but even then there are limitations such as i can't go beyond 1500 molecules with required box dimensions. So how one can about simulating more than 1000 molecules of alkanes r any molecules for that matter? I know that this problem doesn.t occur for water. any help is highly appreciated. Regards Vinoth -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reg: Simulating large number of molecules
On 2010-12-24 11.06, vinothkumar mohanakrishnan wrote: Hi all I want to simulate more than 1000 molecules of say octane r any alkanes in gromacs. after doing a little math i find my box dimensions for the molecules. but when i use genbox to insert multiple molecules in my local system after running some time it says cannot allocate memory but when the same command i gave it in a Linux cluster interactively (HPCE) it goes well and fills the box with required number of molecules and i get the correct density. but even then there are limitations such as i can't go beyond 1500 molecules with required box dimensions. So how one can about simulating more than 1000 molecules of alkanes r any molecules for that matter? I know that this problem doesn.t occur for water. any help is highly appreciated. Regards Vinoth genbox is memory hungry. Try using genconf. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 2010-12-24 11.04, Mark Abraham wrote: On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong temperature coupling to make sure every replica is at its target temperature. I guess I could do it by setting tau_t small in the Nose-hoover T coupling, but there will come the warning in Gromacs. I maxwarned the warning to proceed, and find the temperature is ok, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks a lot. The temperature coupling algorithms are discussed in the literature, when they were derived (citations in GROMACS manual) and subsequently. I suggest you do your own homework there. The use of REMD is more or less irrelevant to the trade-offs when deciding what temperature coupling scheme to use. That is correct, but do not use Berendsen! There is a recent paper from the Garcia group (IIRC) about the effect of Berendsen coupling on REMD sampling. Not good. Mark Best, Qin 2010/12/21 Qin Qiao qiaoqi...@gmail.com mailto:qiaoqi...@gmail.com Dear all, I wonder what will happen in Nose-hoover coupling when tau_t = dt * nsttcouple, while nsttcouple = nstlist. (I used -maxwarn 1 to ignore the Gromacs warning) I tried this setting, to find the temperature is OK, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks in advance. Best, Qin -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Re: [gmx-users] mdrun mpi segmentation fault in high load situation
I'm not sure that PD has any advantage here. From memory it has to create a 128x1x1 grid, and you can direct that with DD also. See mdrun -h -hidden for -dd. Mark The contents of your .log file will be far more helpful than stdout in diagnosing what condition led to the problem. Mark So the only difference is the number of cores I am using. I used -dd but then my system consists only of 4 or slightly more domains which gives me almost no advantage over -pd. The minimum size of a domain is connected to the largest bond length which in my case is half of the box size or more. I will post my .log file but it will probably be next year. So merry christmas and a jolly time. André Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] nve simulation
Dear Gmx users, I wanted to do a simulation with NVE ensemble but i want the temprature to be always around 300k but in my simulation the temp is 380k.can anyone help me out with this. regards, sree. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
Not really, there were no errors with ./configure so I downloaded the version through ubunto sudo -apt get install gromacs but it was old version On Fri, Dec 24, 2010 at 10:53 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 24/12/2010 6:45 PM, Sergio Manzetti wrote: Hi thanks, but if I use make it says make no Makefile found... Right, so configure didn't work, unlike your statement that it did work... Troubleshoot the step that failed, not things that came after it... Mark On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 23/12/2010 9:12 PM, Sergio Manzetti wrote: Dear Users, I am unable to get pass the first step of ./configure . This step works, but when typing make it says: no targets specified and no makefile found. That suggests configure did not work. Should it be like this, or is it compulsory to use cmake? cmake is not compulsory. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 24/12/10 10:36, David van der Spoel wrote: On 2010-12-24 11.04, Mark Abraham wrote: On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong temperature coupling to make sure every replica is at its target temperature. I guess I could do it by setting tau_t small in the Nose-hoover T coupling, but there will come the warning in Gromacs. I maxwarned the warning to proceed, and find the temperature is ok, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks a lot. The temperature coupling algorithms are discussed in the literature, when they were derived (citations in GROMACS manual) and subsequently. I suggest you do your own homework there. The use of REMD is more or less irrelevant to the trade-offs when deciding what temperature coupling scheme to use. That is correct, but do not use Berendsen! There is a recent paper from the Garcia group (IIRC) about the effect of Berendsen coupling on REMD sampling. Not good. Mark I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 2010-12-24 13.15, ms wrote: On 24/12/10 10:36, David van der Spoel wrote: On 2010-12-24 11.04, Mark Abraham wrote: On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong temperature coupling to make sure every replica is at its target temperature. I guess I could do it by setting tau_t small in the Nose-hoover T coupling, but there will come the warning in Gromacs. I maxwarned the warning to proceed, and find the temperature is ok, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks a lot. The temperature coupling algorithms are discussed in the literature, when they were derived (citations in GROMACS manual) and subsequently. I suggest you do your own homework there. The use of REMD is more or less irrelevant to the trade-offs when deciding what temperature coupling scheme to use. That is correct, but do not use Berendsen! There is a recent paper from the Garcia group (IIRC) about the effect of Berendsen coupling on REMD sampling. Not good. Mark I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. V-rescale is a good choice. Berendsen not only gives you the wrong ensemble but it also biases the energy distribution to lower energies. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun mpi segmentation fault in high load situation
On 24/12/2010 9:59 PM, Wojtyczka, André wrote: I'm not sure that PD has any advantage here. From memory it has to create a 128x1x1 grid, and you can direct that with DD also. See mdrun -h -hidden for -dd. Mark The contents of your .log file will be far more helpful than stdout in diagnosing what condition led to the problem. Mark So the only difference is the number of cores I am using. I used -dd but then my system consists only of 4 or slightly more domains which gives me almost no advantage over -pd. The minimum size of a domain is connected to the largest bond length which in my case is half of the box size or more. If it were more than half the box size, then since that restricts the minimum diameter of the DD cell, surely DD would produce a single domain. Either way, it sounds like the ratio of system size to bond length is too small to permit efficient GROMACS-style parallelism. Not all systems are worth parallelising, even if you have a good algorithm for the case at hand... and both DD and PD are targeted at the usual situation in MD where the box size is many times larger than the typical bond length. Mark I will post my .log file but it will probably be next year. So merry christmas and a jolly time. André Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reg: Simulating large number of molecules
On 24/12/2010 9:06 PM, vinothkumar mohanakrishnan wrote: Hi all I want to simulate more than 1000 molecules of say octane r any alkanes in gromacs. after doing a little math i find my box dimensions for the molecules. but when i use genbox to insert multiple molecules in my local system after running some time it says cannot allocate memory but when the same command i gave it in a Linux cluster interactively (HPCE) it goes well and fills the box with required number of molecules and i get the correct density. OK, so I think you've demonstrated that your Linux cluster nodes have more memory available. but even then there are limitations such as i can't go beyond 1500 molecules with required box dimensions. Read genbox -h. Molecules get placed randomly at interstices. Close packings are intrinsically non-random, so you won't get them from random packing. So how one can about simulating more than 1000 molecules of alkanes r any molecules for that matter? I know that this problem doesn.t occur for water. any help is highly appreciated. If you want more molecules, use a bigger box. If you want more molecules at high density, use a bigger box and very careful, very gentle pressure coupling to compress it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] amber convert gromacs input files
Have a good look in acpype, specially its wiki. There you'll see that acpype is totally new code and among other things it covers amb2gmx.pl and solves several of its drawbacks. It's not perfect though but for a system created in tleap, the project is likely to be completed converted to gmx. Alan On 23 December 2010 22:29, Oliver Grant olymacfoo...@gmail.com wrote: Hi, Not sure exactly what you plan to simulate but here are a couple of potential pitfalls: Does acpype call amb2gmx.pl or is it new code that converts? If it is a amb2gmx.pl call I'd check the torsions on the NAc group if you have one. They didn't get translated when I used it. When using amber ports be careful about using default index groups like protein or C alpha as they won't contain atoms from residues like LYP that are different in the ports. Also you'll want to set fudge to 1.0 in the amber99sb.itp or where it is set (can't check this atm) if simulating the sugar alone. Its due to differences in the way amber and glycam are parametrized. (If you are interested it is differences in 1-4 scaling). There may be other issues I'm not aware of yet. :) All the best, Oliver On 23 December 2010 18:13, Alan Wilter Sousa da Silva awil...@ebi.ac.ukwrote: Have a look at acpype.googlecode.com Alan 2010/12/23 gromacs564 gromacs...@126.com Hi , I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam web(they are glycam06 force field,included in AMBER) , but cannot converted this amber files to gromacs files format. Can anyone help me to convert this (amber) files to gromacs input files(top or itp,gro).? Many thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Not really, there were no errors with ./configure That's simply not possible. The purpose of configuration is to determine specifications of your system, which are then used to write the Makefile. If you have no Makefile, then something failed. If you want to try to figure it out, then please post your complete ./configure command and the resulting screen output. Otherwise, your stuck with all of us telling you that something went wrong, but we don't know what. -Justin so I downloaded the version through ubunto sudo -apt get install gromacs but it was old version On Fri, Dec 24, 2010 at 10:53 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 24/12/2010 6:45 PM, Sergio Manzetti wrote: Hi thanks, but if I use make it says make no Makefile found... Right, so configure didn't work, unlike your statement that it did work... Troubleshoot the step that failed, not things that came after it... Mark On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 23/12/2010 9:12 PM, Sergio Manzetti wrote: Dear Users, I am unable to get pass the first step of ./configure . This step works, but when typing make it says: no targets specified and no makefile found. That suggests configure did not work. Should it be like this, or is it compulsory to use cmake? cmake is not compulsory. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
Thanks Justin, here is it the copy-out: ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... no checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... no checking for c++... no checking for gpp... no checking for aCC... no checking for CC... no checking for cxx... no checking for cc++... no checking for cl.exe... no checking for FCC... no checking for KCC... no checking for RCC... no checking for xlC_r... no checking for xlC... no checking whether we are using the GNU C++ compiler... no checking whether g++ accepts -g... no checking dependency style of g++... none checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes configure: creating
Re: [gmx-users] Installation GROMACS UBUNTU
Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks Justin, here is it the copy-out: ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... no checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... no checking for c++... no checking for gpp... no checking for aCC... no checking for CC... no checking for cxx... no checking for cc++... no checking for cl.exe... no checking for FCC... no checking for KCC... no checking for RCC... no checking for xlC_r... no checking for xlC... no checking whether we are using the GNU C++ compiler... no checking whether g++ accepts -g... no checking dependency style of g++... none checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no
Re: [gmx-users] Installation GROMACS UBUNTU
Thanks J, I think I will install Ubuntu entirely first, because I just tried to install FFTW now, and managed only to get to make install, then I got permission denied messages, so even though I thought I was the admin, I am seemingly not. On Fri, Dec 24, 2010 at 2:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks Justin, here is it the copy-out: ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... no checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... no checking for c++... no checking for gpp... no checking for aCC... no checking for CC... no checking for cxx... no checking for cc++... no checking for cl.exe... no checking for FCC... no checking for KCC... no checking for RCC... no checking for xlC_r... no checking for xlC... no checking whether we are using the GNU C++ compiler... no checking whether g++ accepts -g... no checking dependency style of g++... none checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking
Re: [gmx-users] Installation GROMACS UBUNTU
Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks J, I think I will install Ubuntu entirely first, because I just tried to install FFTW now, and managed only to get to make install, then I got permission denied messages, so even though I thought I was the admin, I am seemingly not. Before blowing away your system, use sudo make install, which will prompt you for your password and should work if you actually are an admin. -Justin On Fri, Dec 24, 2010 at 2:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks Justin, here is it the copy-out: ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... no checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... no checking for c++... no checking for gpp... no checking for aCC... no checking for CC... no checking for cxx... no checking for cc++... no checking for cl.exe... no checking for FCC... no checking for KCC... no checking for RCC... no checking for xlC_r... no checking for xlC... no checking whether we are using the GNU C++ compiler... no checking whether g++ accepts -g... no checking dependency style of g++... none checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports
Re: [gmx-users] Installation GROMACS UBUNTU
Thanks again J, is that compulsory each time one installs something new? On Fri, Dec 24, 2010 at 2:50 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks J, I think I will install Ubuntu entirely first, because I just tried to install FFTW now, and managed only to get to make install, then I got permission denied messages, so even though I thought I was the admin, I am seemingly not. Before blowing away your system, use sudo make install, which will prompt you for your password and should work if you actually are an admin. -Justin On Fri, Dec 24, 2010 at 2:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks Justin, here is it the copy-out: ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... no checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... no checking for c++... no checking for gpp... no checking for aCC... no checking for CC... no checking for cxx... no checking for cc++... no checking for cl.exe... no checking for FCC... no checking for KCC... no checking for RCC... no checking for xlC_r... no checking for xlC... no checking whether we are using the GNU C++ compiler... no checking whether g++ accepts -g... no checking dependency style of g++... none checking the maximum length of
Re: [gmx-users] Installation GROMACS UBUNTU
Well here is the FFTW message at make install: /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h' /usr/bin/install: cannot remove `/usr/local/include/fftw3.h': Permission denied /usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f' /usr/bin/install: cannot remove `/usr/local/include/fftw3.f': Permission denied make[3]: *** [install-includeHEADERS] Error 1 make[3]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[1]: *** [install] Error 2 make[1]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
Justin, THe FFTW messagte was AFTER sudo make install. On Fri, Dec 24, 2010 at 2:53 PM, Sergio Manzetti sergio.manze...@vestforsk.no wrote: Well here is the FFTW message at make install: /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h' /usr/bin/install: cannot remove `/usr/local/include/fftw3.h': Permission denied /usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f' /usr/bin/install: cannot remove `/usr/local/include/fftw3.f': Permission denied make[3]: *** [install-includeHEADERS] Error 1 make[3]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[1]: *** [install] Error 2 make[1]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Justin, THe FFTW messagte was AFTER sudo make install. Then you're not an admin. You can always do the installations in your home directory (for both FFTW and Gromacs) by specifying an appropriate --prefix during configuration. -Justin On Fri, Dec 24, 2010 at 2:53 PM, Sergio Manzetti sergio.manze...@vestforsk.no wrote: Well here is the FFTW message at make install: /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h' /usr/bin/install: cannot remove `/usr/local/include/fftw3.h': Permission denied /usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f' /usr/bin/install: cannot remove `/usr/local/include/fftw3.f': Permission denied make[3]: *** [install-includeHEADERS] Error 1 make[3]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[1]: *** [install] Error 2 make[1]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
Thanks, but I will start from scratch. On Fri, Dec 24, 2010 at 3:13 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Justin, THe FFTW messagte was AFTER sudo make install. Then you're not an admin. You can always do the installations in your home directory (for both FFTW and Gromacs) by specifying an appropriate --prefix during configuration. -Justin On Fri, Dec 24, 2010 at 2:53 PM, Sergio Manzetti sergio.manze...@vestforsk.no wrote: Well here is the FFTW message at make install: /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h' /usr/bin/install: cannot remove `/usr/local/include/fftw3.h': Permission denied /usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f' /usr/bin/install: cannot remove `/usr/local/include/fftw3.f': Permission denied make[3]: *** [install-includeHEADERS] Error 1 make[3]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[1]: *** [install] Error 2 make[1]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] simulation at constant temprature
Dear Gmx users, I wanted to do a simulation with NVE ensemble but i want the temprature to be always around 300k but in my simulation the temp is 380k.I am usng leap frog as integrator .can anyone help me out with this.how to do the velocity rescaling regards, sree. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] number of coordinates in coordinate file does not match topology
hello I m unable to update the [ molecules ] directive of topol_pope.top . grompp -f minim.mdp -c system_inflated.gro -p topol_pope.top -o em1.tpr Fatal error: number of coordinates in coordinate file (system_inflated.gro, 20782) does not match topology (topol_pope.top, 37867) this is my .top file ; Include chain topologies #include forcefield.itp #include pope.itp ; Include water topology #include spc.itp ; Include ion topologies #include ions.itp ; System specifications [ system ] 340-Lipid POPE Bilayer [ molecules ] ; molecule name nr. POPE 340 SOL 6729 this is system.gro Gnomes, ROck Monsters And Chili Sauce 41229 this is sytem_inflated.gro What you read here has nothing to do with anything. So you don't have to read it. Thank you. 20782 but there is 3362 protein atom and 17680 lipid in sytem_inflated.gro then why inflategro.pl script is generating wrong total count . help! thank for ur support ! with regards : shikha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] simulation at constant temprature
On Fri, 24 Dec 2010 06:36:03 -0800 sreelakshmi ramesh sree.laks...@research.iiit.ac.in wrote: Dear Gmx users, I wanted to do a simulation with NVE ensemble but i want the temprature to be always around 300k but in my simulation the temp is 380k.I am usng leap frog as integrator .can anyone help me out with this.how to do the velocity rescaling NVE is constant energy, implying the sum of the potential and the kinetic energy is constant. The temperature is only the kinetic part, so it will fluctuate during an NVE run. Constant temperature corresponds to NVT or NPT, in which the system exchanges heat with a heat bath (NPT also has a pressure bath which tries to keep the pressure constant). -- -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] number of coordinates in coordinate file does not match topology
Quoting shikha agarwal shikhaiiit...@gmail.com: hello I m unable to update the [ molecules ] directive of topol_pope.top . grompp -f minim.mdp -c system_inflated.gro -p topol_pope.top -o em1.tpr Fatal error: number of coordinates in coordinate file (system_inflated.gro, 20782) does not match topology (topol_pope.top, 37867) this is my .top file ; Include chain topologies #include forcefield.itp #include pope.itp ; Include water topology #include spc.itp ; Include ion topologies #include ions.itp ; System specifications [ system ] 340-Lipid POPE Bilayer [ molecules ] ; molecule name nr. POPE 340 SOL 6729 this is system.gro Gnomes, ROck Monsters And Chili Sauce 41229 this is sytem_inflated.gro What you read here has nothing to do with anything. So you don't have to read it. Thank you. 20782 but there is 3362 protein atom and 17680 lipid in sytem_inflated.gro then why inflategro.pl script is generating wrong total count . It isn't wrong. Inflategro deletes all water molecules and any lipids that overlap with the protein. You need to update the number of lipid molecules in your topology accordingly. There is also no reference to a protein in your topology. It appears to contain only lipid information, so you're doing something very wrong here. -Justin help! thank for ur support ! with regards : shikha Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] velocity rescaling
what is velocity rescaling and how to use it in nve simulations. thanks in advance. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] velocity rescaling
Quoting sreelakshmi ramesh sree.laks...@research.iiit.ac.in: what is velocity rescaling and how to use it in nve simulations. Velocity rescaling is a method for controlling temperature by modifying the kinetic energy. In an NVE simulation, thermostats are not used. -Justin thanks in advance. Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 24/12/10 12:26, David van der Spoel wrote: I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. V-rescale is a good choice. Berendsen not only gives you the wrong ensemble but it also biases the energy distribution to lower energies. Out of curiosity: why is it still supported in GROMACS? Wouldn't lead to less confusion if it is removed? :) -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 12/24/10 6:40 PM, ms wrote: On 24/12/10 12:26, David van der Spoel wrote: I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. V-rescale is a good choice. Berendsen not only gives you the wrong ensemble but it also biases the energy distribution to lower energies. Out of curiosity: why is it still supported in GROMACS? Wouldn't lead to less confusion if it is removed? :) It's still useful for equilibration, e.g. gas to liquid conversion. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dssp
mustafa bilsel wrote: Hi, I have a problem with dssp programme. I have the programme in /home/m/DSSP. When I write export DSSP=/usr/local/bin and then I check /usr/local/bin I couldn't see dssp. How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written. Could you write export DSSP=/path/to/dssp command according to me. The proper setting for the environment variable is explained in great detail here: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note the line If this is not the case, you must set the DSSP environment variable accordingly, pointing to the actual dssp executable, not just the PATH to it. And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I see the package not found message. What should I do about it? Learn what your shell uses and apply it. You're more than likely running bash, in which case export is the command to use. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] minimization
Dear Justin, I have added your last reply to the end of this message. my shell type is bash. my dssp exe file is in /home/m/DSSP/dssp I wrote export DSSP=//home/m/DSSP/ as in gromacs web page, then I did do_dssp I have the below error. Although the dssp exe is in /usr/local/bin and also I did export, computer couldn't find dssp exe file. What is the problem? What should I do? Best wishes Mustafa - Select a group: 5 Selected 5: 'MainChain' There are 90 residues in your selected group Reading frame 0 time0.000 Back Off! I just backed up ddt2Vei2 to ./#ddt2Vei2.1# --- Program do_dssp, VERSION 4.5.1 Source code file: do_dssp.c, line: 521 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddt2Vei2 ddPcoaqM /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- mustafa bilsel wrote: Hi, I have a problem with dssp programme. I have the programme in /home/m/DSSP. When I write export DSSP=/usr/local/bin and then I check /usr/local/bin I couldn't see dssp. How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written. Could you write export DSSP=/path/to/dssp command according to me. The proper setting for the environment variable is explained in great detail here: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note the line If this is not the case, you must set the DSSP environment variable accordingly, pointing to the actual dssp executable, not just the PATH to it. And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I see the package not found message. What should I do about it? Learn what your shell uses and apply it. You're more than likely running bash, in which case export is the command to use. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] minimization
Hi, What is the meaning of the below message after I completed minimization? Does it mean minimization is successful? In my input parameters nsteps=10,000,000 but minimization stops at about 14,000 th step. Is 10,000,000 very large? What is the typical value for it? And also what is the meaning of Fmax10? Message: Converged to machine precision, but not to the requested precision Fmax10. Best wishes Mustafa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] minimization
mustafa bilsel wrote: Dear Justin, I have added your last reply to the end of this message. my shell type is bash. my dssp exe file is in /home/m/DSSP/dssp I wrote export DSSP=//home/m/DSSP/ as in gromacs web page, then I did This is still wrong. As I quoted in the previous message, the DSSP environment variable has to point to the actual executable, *not* simply the directory that contains it. Therefore: export DSSP=/home/m/DSSP/dssp do_dssp I have the below error. Although the dssp exe is in /usr/local/bin and also I did export, computer couldn't find dssp exe file. What is the problem? What should I do? Probably due to incorrect environment variable settings. -Justin Best wishes Mustafa - Select a group: 5 Selected 5: 'MainChain' There are 90 residues in your selected group Reading frame 0 time0.000 Back Off! I just backed up ddt2Vei2 to ./#ddt2Vei2.1# --- Program do_dssp, VERSION 4.5.1 Source code file: do_dssp.c, line: 521 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddt2Vei2 ddPcoaqM /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- mustafa bilsel wrote: Hi, I have a problem with dssp programme. I have the programme in /home/m/DSSP. When I write export DSSP=/usr/local/bin and then I check /usr/local/bin I couldn't see dssp. How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written. Could you write export DSSP=/path/to/dssp command according to me. The proper setting for the environment variable is explained in great detail here: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note the line If this is not the case, you must set the DSSP environment variable accordingly, pointing to the actual dssp executable, not just the PATH to it. And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I see the package not found message. What should I do about it? Learn what your shell uses and apply it. You're more than likely running bash, in which case export is the command to use. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] minimization
mustafa bilsel wrote: Hi, What is the meaning of the below message after I completed minimization? Does it mean minimization is successful? In my input parameters nsteps=10,000,000 but minimization stops at about 14,000 th step. Is 10,000,000 very large? What is the typical value for it? That depends on the system and how far from the minimum it is. And also what is the meaning of Fmax10? Message: Converged to machine precision, but not to the requested precision Fmax10. Fmax corresponds to the value of the potential energy gradient. I'd suggest some textbook reading here. If you don't understand what EM is doing, you probably shouldn't be running it blindly without knowing what the settings are. -Justin Best wishes Mustafa -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? I'm quite curious how to choose the frequency of the T-coupling in REMD. Though it seems the higher the frequency, the more accurate T will be, I wonder whether it will get artifacts for in MD run.. since the warning in Gromacs says tau_t should be 20 times bigger than dt*nsttcouple.. Best, Qin 2010/12/25 David van der Spoel sp...@xray.bmc.uu.se On 12/24/10 6:40 PM, ms wrote: On 24/12/10 12:26, David van der Spoel wrote: I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. V-rescale is a good choice. Berendsen not only gives you the wrong ensemble but it also biases the energy distribution to lower energies. Out of curiosity: why is it still supported in GROMACS? Wouldn't lead to less confusion if it is removed? :) It's still useful for equilibration, e.g. gas to liquid conversion. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] generate .top file
hello Merry Christmas. this is my topol_pope.top file ; Include chain topologies #include forcefield.itp #include pope.itp ; Include water topology #include spc.itp ; Include ion topologies #include ions.itp ; System specifications [ system ] 340-Lipid POPE Bilayer [ molecules ] ; molecule name nr. POPE 340 SOL 6729 but it should contain protein molecule .what should be topology file ,, how to generate that for system.gro according to tutorial. my protein has 344 molecules . I tried to use g_x2top but it is not available for gromos53a6. help! thank for ur support ! with regards : shikha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pulling
Dear All I want to pull my ligand from protein which is docked to it for generating configurations for umbrella sampling. But my ligand is located in a hole inside of protein. If I pull it along the line which is connecting COMs of them,the ligand may be arrested(constraint)inside of hole. Am I force to pull ligand along this line or I can pull along any line for generating configurations for umbrella sampling? I think the important is to pull it out from the binding pocket and we need to pull it along a line which is connecting the center of pocket(no protein's COM)to ligand's COM. What do you think. Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
