Re: [gmx-users] intermolecular distance restraint

warren deng wrote: Hi Gromacs users, In my simulation, I need to restrain distances between atoms on two protein molecules. But the Gromacs manual on NOE seems to imply that the atom indices belong to the same molecule type. So I am wondering whether it is possible to create distance

Re: [gmx-users] intermolecular distance restraint

Thank you Mark. The problem is, in order to use the couple-moltype option for decoupling, I want to keep the two proteins in separate moleculetype(s). Now I noted that Gromacs has a pull option for doing umbrella sampling, but I don't know how it might be used to apply distance restraint between

Re: [gmx-users] intermolecular distance restraint

Hi Warren, if you want to use distance restraints, the two proteins must be in the same gromacs molecule. AFAIK, it is impossible to use distance restraints between atoms of different molecules. Altermatively, you may want to consider bonds of type 6 (not subject to lincs). pdb2gmx -merge is

Re: [gmx-users] intermolecular distance restraint

Hi Jochen, Thanks a lot for the information, I appreciate. I will merge the two proteins into a single moleculetype and apply the distance restraint, as you suggested. Although I could try use the pull code, I am not sure if they interfere with free energ (lambda) code which I am also using.

[gmx-users] intermolecular distance restraint

Hi Gromacs users, In my simulation, I need to restrain distances between atoms on two protein molecules. But the Gromacs manual on NOE seems to imply that the atom indices belong to the same molecule type. So I am wondering whether it is possible to create distance restraint between two molecule