[gmx-users] How to mention torsional parameter in toplogy

[Tushar Ranjan Moharana]

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