RE: [gmx-users] How to increase the number of parameters in dihedral angle potentials?
Hi, I already answered this mail, but somehow for a small fraction of the mails I reply to hotmail replies to the user, not to the list. Here is my answer: You can't do this easily. The current maximum for the number of parameters per interaction is 6. If you really want to, you could increase this, as well as NR_RBDIHS in include/types/idef.h. This would make your tpr files incompatible with the standard release binaries. Another option would be to use tabulated dihedral functions, then you can do anything you want (see the manual). Berk Date: Tue, 23 Jun 2009 10:16:45 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] How to increase the number of parameters in dihedral angle potentials? bh...@princeton.edu wrote: Dear all, This is the problem I meet with. GROMACS provides a Ryckaert-Bellemans function with 6 parameters (C0, C1, C2, ..., C5) , while what I need is a function of summation over 8 terms, that is, 8 parameters from C0 to C7. I tried to add the values of the two additional pamameters at the end of each lines in the section of dihedral angles in the 'molecule.itp' file. The 'grompp' command then gave an error information, saying there could only be either 6 or 12 parameters for Ryckaert-Bellemans potentials. If you read the description of R-B in the manual, it only allows for 6-parameter R-B. It's not obvious (see footnote to table 5.4, at least), but the other are for free energy calculations that might be varying these parameters. So I added 4 zeros for the rest 4 parameters in 'molecule.itp'. Now, the 'grompp' command did not gave error information any more and I run the simulation with a 12-parameter Ryckaert-Bellemans potential. The problem is that the trajectory obtained from 12-parameter RB potential is exactly the same as the trajectory having generated by 6-parameter RB potential. That means the newly added 6 parameter values can not be recognized by GROMACS. Has anyone met with such kind of problems? Hence, your observations. Since you're not running FE, the 7th and 8th are never being used for anything. What did you do to make GROMACS recognize 6 more parameters in RB potentials? You can't. You would have to either implement your own bonded function, or use a table lookup for this bonded interaction. See manual section 4.2.13 Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to increase the number of parameters in dihedral angle potentials?
Dear all, This is the problem I meet with. GROMACS provides a Ryckaert-Bellemans function with 6 parameters (C0, C1, C2, ..., C5) , while what I need is a function of summation over 8 terms, that is, 8 parameters from C0 to C7. I tried to add the values of the two additional pamameters at the end of each lines in the section of dihedral angles in the 'molecule.itp' file. The 'grompp' command then gave an error information, saying there could only be either 6 or 12 parameters for Ryckaert-Bellemans potentials. So I added 4 zeros for the rest 4 parameters in 'molecule.itp'. Now, the 'grompp' command did not gave error information any more and I run the simulation with a 12-parameter Ryckaert-Bellemans potential. The problem is that the trajectory obtained from 12-parameter RB potential is exactly the same as the trajectory having generated by 6-parameter RB potential. That means the newly added 6 parameter values can not be recognized by GROMACS. Has anyone met with such kind of problems? What did you do to make GROMACS recognize 6 more parameters in RB potentials? Thanks Bingster ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to increase the number of parameters in dihedral angle potentials?
bh...@princeton.edu wrote: Dear all, This is the problem I meet with. GROMACS provides a Ryckaert-Bellemans function with 6 parameters (C0, C1, C2, ..., C5) , while what I need is a function of summation over 8 terms, that is, 8 parameters from C0 to C7. I tried to add the values of the two additional pamameters at the end of each lines in the section of dihedral angles in the 'molecule.itp' file. The 'grompp' command then gave an error information, saying there could only be either 6 or 12 parameters for Ryckaert-Bellemans potentials. If you read the description of R-B in the manual, it only allows for 6-parameter R-B. It's not obvious (see footnote to table 5.4, at least), but the other are for free energy calculations that might be varying these parameters. So I added 4 zeros for the rest 4 parameters in 'molecule.itp'. Now, the 'grompp' command did not gave error information any more and I run the simulation with a 12-parameter Ryckaert-Bellemans potential. The problem is that the trajectory obtained from 12-parameter RB potential is exactly the same as the trajectory having generated by 6-parameter RB potential. That means the newly added 6 parameter values can not be recognized by GROMACS. Has anyone met with such kind of problems? Hence, your observations. Since you're not running FE, the 7th and 8th are never being used for anything. What did you do to make GROMACS recognize 6 more parameters in RB potentials? You can't. You would have to either implement your own bonded function, or use a table lookup for this bonded interaction. See manual section 4.2.13 Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to increase the number of
Thanks to all that answered. I solved the problem with the approach Mark suggested and it seems to be working fine! Thanks Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.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] how to increase the number of
Dear All, I am using GROMACS 3.3.1 and i setup a simulation to run in 2 nodes of a workstation. It is running OK however now i have two extra nodes available to use in the same box and i would like to speed up the sim by using them. Is there any way to increase the number of nodes under use ? I tried tpbconv to extend the sim and increase the np vaue but it did not worked. Thanks Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.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
Re: [gmx-users] how to increase the number of
Afonso Duarte wrote: Dear All, I am using GROMACS 3.3.1 and i setup a simulation to run in 2 nodes of a workstation. It is running OK however now i have two extra nodes available to use in the same box and i would like to speed up the sim by using them. Is there any way to increase the number of nodes under use ? I tried tpbconv to extend the sim and increase the np vaue but it did not worked. The other way to do a restart is to get your original .mdp file (check the values of gen_seed and unconstrained_start are appropriate), and your current .trr, .edr and any appropriate .gro (it's just used for atom names) and feed them to grompp with whatever -n flag you want to use. I expect this will not be reproducible with a tpbconv restart (particularly with PME) but you'll still be sampling the same ensemble within the error of the MD approximation. 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] how to increase the number of
On 5/17/2007 8:14 PM, Afonso Duarte wrote: Dear All, I am using GROMACS 3.3.1 and i setup a simulation to run in 2 nodes of a workstation. It is running OK however now i have two extra nodes available to use in the same box and i would like to speed up the sim by using them. Is there any way to increase the number of nodes under use ? Check your MPICH/LAM implementation about how to boot up the extra nodes. I tried tpbconv to extend the sim and increase the np vaue but it did not worked. tpbconv cannot increase the nodes number. You have to opt for grompp, for which you can also obtain a exact continuation if you have .trr and .edr. Thanks Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.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] how to increase the number of
Oops ! am sorry. but i'm sure i had done this once earlier with some flag, without tinkering with the mdp file. i vaguely remember doing that. shall verify and get back to you. sorry afonso, and thanks for pointing out, mark ! :) regards, Kota. On 5/18/07, Mark Abraham [EMAIL PROTECTED] wrote: Pradeep Kota wrote: Hi Afonso, An easier way would be to use the -time flag with grompp. it would basically set the first time frame for the new tpr to what you give it. jus play around with it and i'm sure you can get what you wanted. dont forget to include the -np flag of course. :) No, that's not what grompp -time is for. See the man page. If you want to pretend it's the same simulation, by having the step numbering start from wherever you're up to, then there is an .mdp flag you can set. See section 7.3 of the manual. 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
