Re: [gmx-users] itp atomtypes section
Hi James, The 6 and 1 are the number of electrons the atomtype has, which is used for QM/MM stuff. Gromacs can tell whether or not it is given by checking the format of the line. If the 5th column is a letter, then the number isn't there, if the 6th column is a letter, it must be there. Hope it helps, Tsjerk On Tue, Nov 27, 2012 at 3:45 AM, James Cannon jamesresearch...@gmail.comwrote: Dear users, I apologise if this is a stupid question, however after a morning of searching I have not been able to find the answer. 1. I have a sample itp file and it contains a section like this: [ atomtypes ] CF CF 6 12.011000.2588 A3.5e-01 2.56134e-01 HF HF 1 1.008000.1000 A3.5e-01 4.28529e-01 I can't work out what the column containing the 6 and 1 is for. Can anyone help? It's not documented anywhere that I can find. 2. I notice that there are many types of atomtypes fields. From the manual: [ atomtypes ] ;name mass charge ptype c6 c12 O 15.99940 0.000 A 0.22617E-02 0.74158E-06 OM 15.99940 0.000 A 0.22617E-02 0.74158E-06 This is clearly a different format to my sample above. Why does the format vary? I know the above format is not wrong because it runs succcessfully in a test-run. How does gromacs know which format to use correctly? I appreciate any help. Thank you. Best regards, James -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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
Re: [gmx-users] itp atomtypes section
Dear Tsjerk, Thanks for clarifying that for me. I appreciate it. Best regards, James On Tue, Nov 27, 2012 at 5:25 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi James, The 6 and 1 are the number of electrons the atomtype has, which is used for QM/MM stuff. Gromacs can tell whether or not it is given by checking the format of the line. If the 5th column is a letter, then the number isn't there, if the 6th column is a letter, it must be there. Hope it helps, Tsjerk On Tue, Nov 27, 2012 at 3:45 AM, James Cannon jamesresearch...@gmail.com wrote: Dear users, I apologise if this is a stupid question, however after a morning of searching I have not been able to find the answer. 1. I have a sample itp file and it contains a section like this: [ atomtypes ] CF CF 6 12.011000.2588 A3.5e-01 2.56134e-01 HF HF 1 1.008000.1000 A3.5e-01 4.28529e-01 I can't work out what the column containing the 6 and 1 is for. Can anyone help? It's not documented anywhere that I can find. 2. I notice that there are many types of atomtypes fields. From the manual: [ atomtypes ] ;name mass charge ptype c6 c12 O 15.99940 0.000 A 0.22617E-02 0.74158E-06 OM 15.99940 0.000 A 0.22617E-02 0.74158E-06 This is clearly a different format to my sample above. Why does the format vary? I know the above format is not wrong because it runs succcessfully in a test-run. How does gromacs know which format to use correctly? I appreciate any help. Thank you. Best regards, James -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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 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] itp atomtypes section
Dear users, I apologise if this is a stupid question, however after a morning of searching I have not been able to find the answer. 1. I have a sample itp file and it contains a section like this: [ atomtypes ] CF CF 6 12.011000.2588 A3.5e-01 2.56134e-01 HF HF 1 1.008000.1000 A3.5e-01 4.28529e-01 I can't work out what the column containing the 6 and 1 is for. Can anyone help? It's not documented anywhere that I can find. 2. I notice that there are many types of atomtypes fields. From the manual: [ atomtypes ] ;name mass charge ptype c6 c12 O 15.99940 0.000 A 0.22617E-02 0.74158E-06 OM 15.99940 0.000 A 0.22617E-02 0.74158E-06 This is clearly a different format to my sample above. Why does the format vary? I know the above format is not wrong because it runs succcessfully in a test-run. How does gromacs know which format to use correctly? I appreciate any help. Thank you. Best regards, James -- 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
