Re: [gmx-users] Charge of CH2r atoms in Gromos 53A6 force-field
OZGE ENGIN wrote: Hi all, I have read the manual of Gromos force field with parameter set 53A6. I am trying to get the topology file of cyclohexane molecule. In a paper which defined the parameters of Gromos 53A5 and 53A6 force-fields, it is said that atoms that are not listed have a zero charge, and the charge of CH2r atoms have not been given in that list. So,to be sure I want to ask again. The charge of CH2r atoms (CH2 groups in a ring) have a zero charge in Gromos 53A6 force-field? What other charge would you like to use in a united-atom model on the six identical CH2R atoms to achieve a neutral cyclohexane molecule? :-) Mark ___ 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] Charge of CH2r atoms in Gromos 53A6 force-field
Hi Ozge, First of all, this is not the GROMOS force field user list. Second, if they state in the manual that atoms that are not listed have zero charge, then they probably have zero charge. Third, since each CH2 in cyclohexane is equivalent to all others, with a bit of chemical intuition it's not that hard to imagine what the charge of a CH2 group will be in that setting... Tsjerk On 9/4/07, OZGE ENGIN <[EMAIL PROTECTED]> wrote: > Hi all, > > I have read the manual of Gromos force field with parameter set 53A6. I am > trying to get the topology file of cyclohexane molecule. > > In a paper which defined the parameters of Gromos 53A5 and 53A6 force-fields, > it is said that atoms that are not listed have a zero charge, and the charge > of CH2r atoms have not been given in that list. So,to be sure I want to ask > again. The charge of CH2r atoms (CH2 groups in a ring) have a zero charge in > Gromos 53A6 force-field? > > thanks > Oz. > > ___ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] Charge of CH2r atoms in Gromos 53A6 force-field
Hi all, I have read the manual of Gromos force field with parameter set 53A6. I am trying to get the topology file of cyclohexane molecule. In a paper which defined the parameters of Gromos 53A5 and 53A6 force-fields, it is said that atoms that are not listed have a zero charge, and the charge of CH2r atoms have not been given in that list. So,to be sure I want to ask again. The charge of CH2r atoms (CH2 groups in a ring) have a zero charge in Gromos 53A6 force-field? thanks Oz. ___ 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
