[gmx-users] How are the charges of the gromos96 forcefiel calculated ?
Dear users, I'm trying to find out how the atoms charges in the GROMOS96 force field were calculated but I've not been able to find out in the manual or in the paper I saw so far. I know that the force fields for MM have the atoms charges calculated by ab initio mathods but I wonder with method was used to GROMOS96. Was it B3LYP 6-31G* in the same way as for OPLSaa ? Thanks for helping. Tanos C. C. Franca. -- 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] Triple bond
Dear users, We ve been trying unsucessfully to perform some MD simulations with some compounds containing triple bonds using GROMACS. Does someone know how to properly construct the topologies to this kind of bond for GROMACS ? With my best regards, Tanos C. C. Franca. -- 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] Error mesage
Dear gmx users, Does someone know how to deal with the error mesage bellow ? With my best regards, Tanos C. C. Franca. Program mdrun, VERSION 4.5.4 Source code file: domdec_con.c, line: 693 Fatal error: DD cell 2 1 0 could only obtain 273 of the 275 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. -- 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] Error mesage
Dear gmx users, Does someone know how to deal with the error mesage bellow ? With my best regards, Tanos C. C. Franca. Program mdrun, VERSION 4.5.4 Source code file: domdec_con.c, line: 693 Fatal error: DD cell 2 1 0 could only obtain 273 of the 275 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. -- 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] Charges
Dear gmx users, Does someone know in which file GROMACS store the information on the protein charge. I've seen that after running pdb2gmx or grompp the system charge is shown in the screen but we would like to know if this information is recorded in some file. With my best regards, Tanos C. C. Franca. Coordinator of the Graduate Program in Chemistry. Military Institute of Engineering Rio de Janeiro - RJ Brazil. -- 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] Help with the heme group in forcefield gromos53a6
Dear users, We are trying to perform a MD simulation of a protein with a heme group using the gromos53a6 force field but, when trying to run grompp, we receive the error mesage: Program grompp, VERSION 4.0.3 Source code file: ../../../../src/kernel/toppush.c, line: 947 Fatal error: Atomtype FE2+ not found How can it happen if the gromos53a6 force field have parameters to the heme group ? Does someone knows how to fix it ? Tanos Celmar Costa Franca - D.Sc Coordenador do Programa de Pos-graduacão em Química Secão de Engenharia Química - SE/5 Instituto Militar de Engenharia - IME Rio de Janeiro - RJ Brasil -- 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] file heme.rtp
Dear Gromacs users, I'm sure that the Gromos5A36 force field have topology to the heme group and would like to know how to proceed to perform a successfull MD simulation on a protein with this group. Should I just write the name of the heme topology file inside the protein.top file (just like we do with ions.itp) ? We also would like to confirm the name of the heme topology file. Is it heme.rtp ? Thank you in advance. Tanos C. C. Franca. Coordinator of the Graduate Program in Chsmistry. Military Intitute of Engineering. Rio de Janeiro - RJ Brazil. -- 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] How to include FE2+ in ions.itp ?
Dear GROMACS users, We're trying to perform a MD simulation of a system with a hematin group but realized that GROMACS does not have parameters for the ion FE2+. We tried to include the parametrs in the file ions.itp but did not suceed yet. Does anybody knows the right procedure to introduce this ions into the file ions.itp ? Do we have to change anything more in order to GROMACS recognize the new ion ? With my best regards, Tanos C. C. Franca. Coordinator of the Graduate Program in Chemistry Military Institute of Engineering. Rio de Janeiro/RJ Brazil. Em 05/01/2011 10:47, gmx-users-requ...@gromacs.org escreveu: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Library file in.m2p not found (Justin A. Lemkul) 2. Warning about (short) potential interruption - movingDNS servers for gromacs.org (Erik Lindahl) 3. Re: Library file in.m2p not found (ahmet y?ld?r?m) 4. HFIP solvent box... (sharada) 5. Re: HFIP solvent box... (Justin A. Lemkul) -- Message: 1 Date: Wed, 05 Jan 2011 06:45:52 -0500 From: Justin A. Lemkuljalem...@vt.edu Subject: Re: [gmx-users] Library file in.m2p not found To: Discussion list for GROMACS usersgmx-users@gromacs.org Message-ID:4d2459f0.2020...@vt.edu Content-Type: text/plain; charset=ISO-8859-9; format=flowed ahmet yýldýrým wrote: Dear Mark, I am using the Gromacs on the Ubuntu for month but have not encountered any problems.I did a search in the file system of Ubuntu. I do not have a GMXLIB folder in a file system. What should I do? If you're telling xpm2ps to use in.m2p, that file has to exist somewhere. The error message is telling you that it does not exist in the working directory (i.e., the directory where you're issuing the command), or the standard Gromacs library directory (http://www.gromacs.org/Documentation/Terminology/Environment_Variables#GMXLIB). If you tell any Gromacs tool to use certain input, it has to exist; Gromacs isn't going to magically create all the proper files for you. -Justin 05 Ocak 2011 10:42 tarihinde Mark Abrahammark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au yazdý: On 5/01/2011 7:37 PM, ahmet yýldýrým wrote: Dear users, I receive the following error when I entered the command xpm2ps -f ss.xpm -o ss.eps -di in.m2p Fatal error: Library file in.m2p not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) I am using the Gromacs 4.05 on the Ubuntu 9.1 Operation System. I installed the Gromacs from Synaptic Package Manager. I used echo $GMXDATA but it did not show anything. The pdb2gmx, g_gyrate,...etc files are in the directory /usr/bin/. The GMXRC file is in the directory /usr/share/gromacs/shell-specific. Are you following these instructions? http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation Mark -- gmx-users mailing listgmx-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 -- Ahmet YILDIRIM -- 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
