Re: [gmx-users] Tabulated potentials for dihedrals - regd
On 7/06/2012 4:33 AM, ramesh cheerla wrote: Dear Mark, Thank you for your reply, According to my understanding functional form of dihedral function type 9 is same as dihedral function type 1 i.e k (1 + cos(n (phi)- phi s)) except the difference that function type 9 is used to handle the multiple potential functions to be applied to the single dihedreal, Is my understanding correct ?. The functional form that I am using Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 is different from the k (1 + cos(n (phi)- phi s)). I am suspecting can I use function type 9 for my function. Can you please clarify my doubt. I said last time you can use type 9. You can use high-school maths to express your equation in the form of a sum of multiple type 1, which is type 9. The additive constant only affects the total energy, which is never used for the simulation. The derivative of V is used, so the constant goes away. Mark Thank you in advance. On Mon, Jun 4, 2012 at 12:55 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 4/06/2012 3:46 AM, ramesh cheerla wrote: Dear Gromacs experts, I am planing to use tabulated potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . I have three different K values (i.e K1,K2,K3 ) one for each 'n' value ( Here 'n' is multiplicity). You do not need a table for this - type 9 will do the job easily, and for friendly values of phi0, there exists an equivalent form to the above that can be expressed as a Ryckaert-Belleman dihedral. See various places of manual chapters 4 and 5. I have generated table and given the table number in dihedrals directive of the ffbonded.itp file, According to my understanding one has to supply K ( force constant ) value in addition to table number in topology. In my case I have three different K values, which k value do I have to take, Can I take sum of all the three k values or can I take arbitrary value. Your table would need to be the weighted sum of the three cosines, so apparently you have not yet generated such a table. But rather than buy trouble, go and do the easier and faster solutions above :-) Mark -- gmx-users mailing list gmx-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 -- 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] Tabulated potentials for dihedrals - regd
Dear Mark, I am very Thankful to you for your valuable suggestion. On Thu, Jun 7, 2012 at 12:04 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 7/06/2012 4:33 AM, ramesh cheerla wrote: Dear Mark, Thank you for your reply, According to my understanding functional form of dihedral function type 9 is same as dihedral function type 1 i.e k (1 + cos(n (phi)- phi s)) except the difference that function type 9 is used to handle the multiple potential functions to be applied to the single dihedreal, Is my understanding correct ?. The functional form that I am using Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 is different from the k (1 + cos(n (phi)- phi s)). I am suspecting can I use function type 9 for my function. Can you please clarify my doubt. I said last time you can use type 9. You can use high-school maths to express your equation in the form of a sum of multiple type 1, which is type 9. The additive constant only affects the total energy, which is never used for the simulation. The derivative of V is used, so the constant goes away. Mark Thank you in advance. On Mon, Jun 4, 2012 at 12:55 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/06/2012 3:46 AM, ramesh cheerla wrote: Dear Gromacs experts, I am planing to use tabulated potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . I have three different K values (i.e K1,K2,K3 ) one for each 'n' value ( Here 'n' is multiplicity). You do not need a table for this - type 9 will do the job easily, and for friendly values of phi0, there exists an equivalent form to the above that can be expressed as a Ryckaert-Belleman dihedral. See various places of manual chapters 4 and 5. I have generated table and given the table number in dihedrals directive of the ffbonded.itp file, According to my understanding one has to supply K ( force constant ) value in addition to table number in topology. In my case I have three different K values, which k value do I have to take, Can I take sum of all the three k values or can I take arbitrary value. Your table would need to be the weighted sum of the three cosines, so apparently you have not yet generated such a table. But rather than buy trouble, go and do the easier and faster solutions above :-) 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/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 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] Tabulated potentials for dihedrals - regd
Dear Mark, Thank you for your reply, According to my understanding functional form of dihedral function type 9 is same as dihedral function type 1 i.e k (1 + cos(n (phi)- phi s)) except the difference that function type 9 is used to handle the multiple potential functions to be applied to the single dihedreal, Is my understanding correct ?. The functional form that I am using Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 is different from the k (1 + cos(n (phi)- phi s)). I am suspecting can I use function type 9 for my function. Can you please clarify my doubt. Thank you in advance. On Mon, Jun 4, 2012 at 12:55 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/06/2012 3:46 AM, ramesh cheerla wrote: Dear Gromacs experts, I am planing to use tabulated potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . I have three different K values (i.e K1,K2,K3 ) one for each 'n' value ( Here 'n' is multiplicity). You do not need a table for this - type 9 will do the job easily, and for friendly values of phi0, there exists an equivalent form to the above that can be expressed as a Ryckaert-Belleman dihedral. See various places of manual chapters 4 and 5. I have generated table and given the table number in dihedrals directive of the ffbonded.itp file, According to my understanding one has to supply K ( force constant ) value in addition to table number in topology. In my case I have three different K values, which k value do I have to take, Can I take sum of all the three k values or can I take arbitrary value. Your table would need to be the weighted sum of the three cosines, so apparently you have not yet generated such a table. But rather than buy trouble, go and do the easier and faster solutions above :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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
Re: [gmx-users] Tabulated potentials for dihedrals - regd
On 4/06/2012 3:46 AM, ramesh cheerla wrote: Dear Gromacs experts, I am planing to use tabulated potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . I have three different K values (i.e K1,K2,K3 ) one for each 'n' value ( Here 'n' is multiplicity). You do not need a table for this - type 9 will do the job easily, and for friendly values of phi0, there exists an equivalent form to the above that can be expressed as a Ryckaert-Belleman dihedral. See various places of manual chapters 4 and 5. I have generated table and given the table number in dihedrals directive of the ffbonded.itp file, According to my understanding one has to supply K ( force constant ) value in addition to table number in topology. In my case I have three different K values, which k value do I have to take, Can I take sum of all the three k values or can I take arbitrary value. Your table would need to be the weighted sum of the three cosines, so apparently you have not yet generated such a table. But rather than buy trouble, go and do the easier and faster solutions above :-) 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/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] Tabulated potentials for dihedrals - regd
Dear Gromacs experts, I am planing to use tabulated potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . I have three different K values (i.e K1,K2,K3 ) one for each 'n' value ( Here 'n' is multiplicity). I have generated table and given the table number in dihedrals directive of the ffbonded.itp file, According to my understanding one has to supply K ( force constant ) value in addition to table number in topology. In my case I have three different K values, which k value do I have to take, Can I take sum of all the three k values or can I take arbitrary value. Any help please. Thank you in advance. Regards, Ramesh. -- 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] tabulated potentials for dihedrals - regd
Dear Gromacs users, I am using tabulated potentials for the dihedrals of my system, the dihedral function I am using is Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . The C-O-C-C dihedral of my system has three folds those are n= 1 , 2, 3 and three different K ( force constant ) values one for each n value. Here my doubt is while specifying the k value in the ffbonded.itp , Which K value do I have to take ? or can i take sum of all these k values and mention that value in ffbonded.itp ? Please help me in this regard, Thank you in advance, Regards, Ramesh cheerla. -- 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
