RE: [gmx-users] Problem with tabulated potentials for 3 different atoms
> From: mrvartore...@gmail.com > Date: Tue, 20 Apr 2010 06:33:09 -0300 > To: gmx-users@gromacs.org > Subject: [gmx-users] Problem with tabulated potentials for 3 different atoms > > Berk: > > Thanks for the help, and thanks too to the other members of the list > who helped me. My simulation is working now with some energy problems, > but this is another problem not related to the software. The missing > space characters were a typing mistake. > > About drugs and other subjets of your post, they are all out of my > research interests. Maybe you wanted to say these to another user? This was intended as a subtle hint to list members in general to keep the discussions polite and constructive. Berk > > Martin. > -- > 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 _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop-- 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] Problem with tabulated potentials for 3 different atoms
Berk: Thanks for the help, and thanks too to the other members of the list who helped me. My simulation is working now with some energy problems, but this is another problem not related to the software. The missing space characters were a typing mistake. About drugs and other subjets of your post, they are all out of my research interests. Maybe you wanted to say these to another user? Martin. -- 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] Problem with tabulated potentials for 3 different atoms
Hi, I don't want to get into discussions on drugs and I don't know if you already switched package, but I'l post my answer anyhow. The energy groups in each pair on your energygrp_table line should be separated by a space. The table files should contain all columns, unused columns are allowed to contain zero's, since they are simply ignored. PS: Please don't mail me directly with questions on Gromacs, apart from the good reasons already given on the list, this is a strong incentive for me not to answer your mail. Berk > From: mrvartore...@gmail.com > Date: Mon, 19 Apr 2010 10:05:59 -0300 > To: gmx-users@gromacs.org > Subject: [gmx-users] Problem with tabulated potentials for 3 different atoms > > I'm trying to use tabulated potentials for a very simple system: a > polymer chain with only 3 kind of atoms: A, B and C, all of it with > zero charge. > > A--(B)n--C > > The only interactions that accounts are AB, AC, BB and CC, so in my > mdp file I have writen: > > coulombtype = user > vdw-type= user > energygrps = A B C > energygrp_table = AB AC BB BC > > Also, I'm using tabulated bonded potentials for bonds and angles. > > The main questions are how to tell to mdrun that he must read my table > files and can I be sure that the reading is OK? > > For the bonding part I have the following table files: > > table_b1.xvg > table_a1.xvg > table_a2.xvg > table_a3.xvg > > And in the mdrun commandline I'm using the option -tableb table. > But how to handle the non bonding table files? > > table_A_B.xvg > table_A_C.xvg > table_B_B.xvg > table_B_C.xvg > > Must I write > > energygrps = A B C > energygrp_table = AC BB BC > > in the mdp file and use the tables > > table.xvg > table_A_C.xvg > table_B_B.xvg > table_B_C.xvg > > with the command line for mdrun saying -table table.xvg? > > Another thing, because the tables doesn't have to contain only zero columns... > Can I put anything on the f and f' columns (because the charge of my > atoms is zero)? > Can I put (for example) 0.5 in the g and g' columns and my potential > (and the force) minus 0.5 in columns h and h'? > > I'm using the 4.0.7 version. > > Again as an abstract: > > System: 1 chain A--(B)n--C > Bonds: A-B = B-B = B-C --> only one table: table_b1.xvg > Angles: A-B-B, B-B-B, B-B-C --> 3 tables: table_a1.xvg, table_a2.xvg, > table_a3.xvg > Charges: none > VDW interactions: A-B, A-C, B-B, B-C --> 4 tables table_A_B.xvg, > table_A_C.xvg, table_B_B.xvg, table_B_C.xvg > > *.mdp lines: > coulombtype = user > vdw-type= user > energygrps = A B C > energygrp_table = ? > > run commandline: > mdrun -s -c -e -x -g -table ? -tableb ? > > Any help will be appreciated. > > Thank you. > > Martin R. Vartorelli > -- > 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
Re: [gmx-users] Problem with tabulated potentials for 3 different atoms
Dear Martin As Mark has already told you - if you have a problem with gromacs email the list and wait for a reply. Don't just email people you don't know from Adam and expect them to reply because "you are in a rush." The file that you have read from the mailing list contains everything I know about tabulated potentials in gromacs. I can't say I fully understand your email but I think that your questions (other than the stuff on bonded potentials) are all covered on the wikki page and certainly are covered in the pdf file I wrote. In short >For the bonding part I have the following table files: >table_b1.xvg >table_a1.xvg >table_a2.xvg >table_a3.xvg I know nothing about using tabulated potentials for bonded interactions. If this is what is in the manual though its probably right. > Must I write > > energygrps = A B C > energygrp_table = AC BB BC > > in the mdp file and use the tables > > table.xvgThis has the A B interaction in? > table_A_C.xvg > table_B_B.xvg > table_B_C.xvg > > with the command line for mdrun saying -table table.xvg? > Yes this is exactly what the wikki tells you to do. Why do you think it wont work in your case? Incidentally, you can work out if this is working by doing one md step in gromacs and comparing the energy you obtain with the energy you get from another code, which you are confident produces correct energies. Another thing, because the tables doesn't have to contain only zero > columns... > Can I put anything on the f and f' columns (because the charge of my > atoms is zero)? > Yes. I always use f=1/r even though I know it will be ignored (with this choice f'=1/r**2 obviously) > Can I put (for example) 0.5 in the g and g' columns and my potential > (and the force) minus 0.5 in columns h and h'? > I don't understand what you want to do here. If you put 0.5 in g then g'=0, which you can work out using, what I assume, is the first thing you learnt about calculus. ciao Gareth -- 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] Problem with tabulated potentials for 3 different atoms
I'm trying to use tabulated potentials for a very simple system: a polymer chain with only 3 kind of atoms: A, B and C, all of it with zero charge. A--(B)n--C The only interactions that accounts are AB, AC, BB and CC, so in my mdp file I have writen: coulombtype = user vdw-type = user energygrps = A B C energygrp_table = AB AC BB BC Also, I'm using tabulated bonded potentials for bonds and angles. The main questions are how to tell to mdrun that he must read my table files and can I be sure that the reading is OK? For the bonding part I have the following table files: table_b1.xvg table_a1.xvg table_a2.xvg table_a3.xvg And in the mdrun commandline I'm using the option -tableb table. But how to handle the non bonding table files? table_A_B.xvg table_A_C.xvg table_B_B.xvg table_B_C.xvg Must I write energygrps = A B C energygrp_table = AC BB BC in the mdp file and use the tables table.xvg table_A_C.xvg table_B_B.xvg table_B_C.xvg with the command line for mdrun saying -table table.xvg? Another thing, because the tables doesn't have to contain only zero columns... Can I put anything on the f and f' columns (because the charge of my atoms is zero)? Can I put (for example) 0.5 in the g and g' columns and my potential (and the force) minus 0.5 in columns h and h'? I'm using the 4.0.7 version. Again as an abstract: System: 1 chain A--(B)n--C Bonds: A-B = B-B = B-C --> only one table: table_b1.xvg Angles: A-B-B, B-B-B, B-B-C --> 3 tables: table_a1.xvg, table_a2.xvg, table_a3.xvg Charges: none VDW interactions: A-B, A-C, B-B, B-C --> 4 tables table_A_B.xvg, table_A_C.xvg, table_B_B.xvg, table_B_C.xvg *.mdp lines: coulombtype = user vdw-type = user energygrps = A B C energygrp_table = ? run commandline: mdrun -s -c -e -x -g -table ? -tableb ? Any help will be appreciated. Thank you. Martin R. Vartorelli -- 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
