[gmx-users] Nucleotides for charmm port
Hi all, Has anybody managed to use ATP with the charmm27 ff in gromacs 4.5? The forcefield files are missing atom and bond types and angle information. This is available for charmm, but I have only found it in stream file and have no idea how to convert it. It should be possible (for someone smarter than me). cheers Dave -- 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
e: [gmx-users] Nucleotides for charmm port
gmx-users-requ...@gromacs.org wrote: 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. Nucleotides for charmm port (David Parcej) 2. Umbrella sampling question (Aswathy) 3. Re: WHAM (Justin A. Lemkul) 4. Re: Nucleotides for charmm port (Thomas Piggot) 5. Re: ARG Charmm gmx 4.5.1 (Thomas Piggot) 6. RE: ARG Charmm gmx 4.5.1 (Berk Hess) -- Message: 1 Date: Fri, 17 Sep 2010 11:44:08 +0200 From: David Parcej par...@biochem.uni-frankfurt.de Subject: [gmx-users] Nucleotides for charmm port To: gmx-users@gromacs.org Message-ID: 4c933868.4020...@biochem.uni-frankfurt.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi all, Has anybody managed to use ATP with the charmm27 ff in gromacs 4.5? The forcefield files are missing atom and bond types and angle information. This is available for charmm, but I have only found it in stream file and have no idea how to convert it. It should be possible (for someone smarter than me). cheers Dave Thank a lot Tom, it worked fine! Dave -- 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] compilation problem: gromacs 4.5 double precision
Hi all. I have a problem building the double (but not single) precision version of gromacs 4.5 on an AMD instanbul based system. compiler is gcc3.4, configure line: ./configure --prefix=/home/gromacs451 -program-suffix=_d --disable-float --enable-double and the error: In file included from nb_kernel400_x86_64_sse2.c:24: ../../../../include/gmx_sse2_double.h: In function `gmx_mm_sincos_pd': ../../../../include/gmx_sse2_double.h:457: warning: implicit declaration of function `_mm_castsi128_pd' ../../../../include/gmx_sse2_double.h:457: error: invalid initializer ../../../../include/gmx_sse2_double.h:514: error: incompatible type for argument 1 of `_mm_and_pd' ../../../../include/gmx_sse2_double.h:515: error: incompatible type for argument 1 of `_mm_andnot_pd' ../../../../include/gmx_sse2_double.h:516: error: incompatible type for argument 1 of `_mm_and_pd' ../../../../include/gmx_sse2_double.h:517: error: incompatible type for argument 1 of `_mm_andnot_pd' make[5]: *** [nb_kernel400_x86_64_sse2.lo] Error 1 Any ideas? cheers Dave - -- 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] Re:J-walking REMD
gmx-users-requ...@gromacs.org wrote: Thanks for the info Mark. Dear All Some time ago there was a discussion concerning the problems of REMD for large systems and the possibility of using the REST implementation of the method. Mark, you mentioned that you had coded an implementation Okur method (JCTC, 2006, 2, 420). How did it work and can you make this available? Any other thoughts on REMD for large systems are also appreciated. I still have my implementation, but didn't use it in anger. Reworking it for GROMACS 4 and using it is on my short-term to-do list. 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] J-walking REMD
Dear All Some time ago there was a discussion concerning the problems of REMD for large systems and the possibility of using the REST implementation of the method. Mark, you mentioned that you had coded an implementation Okur method (JCTC, 2006, 2, 420). How did it work and can you make this available? Any other thoughts on REMD for large systems are also appreciated. cheers David -- - Dr David Parcej, Goethe Universitat Frankfurt, Institut für Biochemie, Biozentrum N210/1.04, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany - -- 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
