Re: [gmx-users] How to mention torsional parameter in toplogy
Hi Mark, Thanks for you valuable advice. Your advice about tabulated entry was very helpful. As you said I read chapter 4 and 5 of manual. Since the equation used in the paper doesn't match any of the standard type mentioned in the manual, I have to use tabulated entry. I have 2 question in this regard. 1) As mentioned in the manual I have to make a .xvg file with 3 column and value of x (in my case angle) should be equally spaced. I just want to know what should be the ideal spacing. Is 10 degree increment or I should go for 1 degree? 2) In the paper they apply angular potential (v(x)=1.3(1+cos(x between the plane defined by atom 1, 2, 3 and 3, 4, 5. I couldn't understand how to mention this in topology. All dihedral involves 4 atoms but here I have 5 atom. 1---2 \ 3 --- 4 \ 5 Thank you for your time and effort. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to mention torsional parameter in toplogy
Hi, The functional forms available are in chapter 4 of the reference manual, and the way to specify the parameters is in chapter 5. So perhaps after some trig, you should be good to work that out (if not, then tabulated bonded interactions are also possible). Make a trivial test case whose energy will tell you that things are working like you expect. Mark On Thu, Jul 2, 2015 at 11:45 PM Tushar Ranjan Moharana < tusharranjanmohar...@gmail.com> wrote: > Hi everyone, > > I want to simulate polyunsaturated fatty acid in GROMOS force field. I want > to consider certain torsional potential (as described by Michal Bachar et. > al. http://pubs.acs.org/doi/full/10.1021/jp036981u). In the paper they > have > mentioned following potential functions which they got from quantum > mechanical calculations (in original paper there was some mistakes in the > equations which later got corrected, I am writing the revised equations) > > V(φ1) = 3.350[1 + cos(φ1-180)] - 1.660 [1 + cos(2φ1-180)] + 7.333 [1 - > cos(3φ1-180)] > > V(φ2) = -5.685 + 7.470 [1 + cos(φ2 - 180)] + 3.900 [1 + cos(2φ2)] + 1.100 > [1 + cos(3φ2)] > > V(φ3) = 0.034617 [φ3]^ 2 > > > V(φ4) = -3.500 + 4.533 [1 + cos(φ4 - 180)] + 3.000 [1 + cos(2φ4)] + 1.550 > [1 + cos(3φ4)] + 1.300 [1 + cos(Θ)] > > Where φ1 to φ4 are shown in following figure and Θ is the torsion angle > between the vectors defined by the two double bonds. Now my problem is How > I will use these potential function in my simulation. I guess I have to > define some [ dihedrals ] and [ exclusions ] but I am confused what exactly > the line will be in the [ dihedrals ] section of the topology. > Any suggestion will be most appreciable. Thanks for your valuable time. > [image: Inline image 1] > > > > > "A society with free knowledge is better than a society with free food" > > Tushar Ranjan Moharana > B. Tech, NIT Warangal > Ph D Student, CCMB > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to mention torsional parameter in toplogy
Hi everyone, I want to simulate polyunsaturated fatty acid in GROMOS force field. I want to consider certain torsional potential (as described by Michal Bachar et. al. http://pubs.acs.org/doi/full/10.1021/jp036981u). In the paper they have mentioned following potential functions which they got from quantum mechanical calculations (in original paper there was some mistakes in the equations which later got corrected, I am writing the revised equations) V(φ1) = 3.350[1 + cos(φ1-180)] - 1.660 [1 + cos(2φ1-180)] + 7.333 [1 - cos(3φ1-180)] V(φ2) = -5.685 + 7.470 [1 + cos(φ2 - 180)] + 3.900 [1 + cos(2φ2)] + 1.100 [1 + cos(3φ2)] V(φ3) = 0.034617 [φ3]^ 2 V(φ4) = -3.500 + 4.533 [1 + cos(φ4 - 180)] + 3.000 [1 + cos(2φ4)] + 1.550 [1 + cos(3φ4)] + 1.300 [1 + cos(Θ)] Where φ1 to φ4 are shown in following figure and Θ is the torsion angle between the vectors defined by the two double bonds. Now my problem is How I will use these potential function in my simulation. I guess I have to define some [ dihedrals ] and [ exclusions ] but I am confused what exactly the line will be in the [ dihedrals ] section of the topology. Any suggestion will be most appreciable. Thanks for your valuable time. [image: Inline image 1] "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
