Re: [gmx-users] topology treatment in free energy calculations -possible bug
Berk Thanks for the clarification. I was aware of A-values copied to B-values, when no B-values in the FF exist, but actually this was new to me. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Berk Hess wrote: This behavior is itentional. But it can indeed be confusing. Therefore in Gromacs 4.0 a warning will be generated (and I have added a table in the manual that explains all the possible combinations). If you explicitly define parameters for the A-state, I don't see why you would want the B-parameters to be looked up based on atom-type. You would only want that when the A-state parameters are also determined by the atom type. Berk. From: Maik Goette [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: GMX-mailinglist gmx-users@gromacs.org Subject: [gmx-users] topology treatment in free energy calculations -possible bug Date: Fri, 04 Jan 2008 15:15:57 +0100 Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ 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 _ Live Search, for accurate results! http://www.live.nl ___ 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
[gmx-users] topology treatment in free energy calculations - possible bug
Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ 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] topology treatment in free energy calculations - possible bug
On Fri, 4 Jan 2008, Maik Goette wrote: Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? it cannot be called as a bug... when you mention parameters for A state in topology explicitly then grompp will expect you to mention the B state parameters also, and if it doesn't find it, it will assign A state parameter to B state. that is quite well documented, i think, in manual. So there is no reason to think it as a bug. bharat Regards -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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] topology treatment in free energy calculations - possible bug
Maik I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 I *think* this behavior is described in the documentation. Basically, anytime A state parameters are specified in the topology and B state are omitted, A state are copied to B state. To make B state different, you have to either (a) specify them explicitly, or (b) have them looked up in the force field where they are different. So this is expected behavior. David Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ 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] topology treatment in free energy calculations -possible bug
This behavior is itentional. But it can indeed be confusing. Therefore in Gromacs 4.0 a warning will be generated (and I have added a table in the manual that explains all the possible combinations). If you explicitly define parameters for the A-state, I don't see why you would want the B-parameters to be looked up based on atom-type. You would only want that when the A-state parameters are also determined by the atom type. Berk. From: Maik Goette [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: GMX-mailinglist gmx-users@gromacs.org Subject: [gmx-users] topology treatment in free energy calculations -possible bug Date: Fri, 04 Jan 2008 15:15:57 +0100 Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ 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 _ Live Search, for accurate results! http://www.live.nl ___ 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
