[gmx-users] free energy and UB term

Dear GMXers, I'm trying to manually add two sets of Urey-Bradley terms to the topology file (in [angle] entry with type 5). However, it seems it is not allowed. I got the following error: Incorrect number of parameters - found 8, expected 4 or 4 for U-B. Is it true that I can't do this in

[gmx-users] nrexcl = 2 or 3?

Dear GMXers, I need to use charmm ff (same question for amber ffs), and am confused with what value I should give to nrexcl in [ moleculetype ], 2 or 3? According to the manual (v 4.5), nrexcl = 3 stands for excluding non-bonded interactions between atoms that are no further than 3 bonds away.

[gmx-users] restraints between two molecules

Dear GMXers, I can apply harmonic bond, angle, and dihedral restraints between two molecules (3 atoms on one, and one atom on the other one). If yes, how to set it up in the topology file? Question 2: Can I apply distance restraint between mass center of some atoms in one molecule and ONE ATOM

[gmx-users] Re: restraints between two molecules

-- lq z wrote: * Dear GMXers,** ** I can apply harmonic bond, angle, and dihedral restraints between two ** molecules (3 atoms on one, and one atom on the other one). If yes, how ** to set it up in the topology file?** * They have to be in the same [moleculetype]. * Question 2: Can I apply

[gmx-users] proper dihedral scaling in free energy simulation

The current scheme for the proper dihedral scaling for free energy simulation assumes the same multiplicity for both states. This is problematic if we want to change, e.g., a CH3 group to an NO2 group. We can manipulate the topology file to make it right. However, it is not general and can be