[gmx-users] intermolecular distance restraint

warren deng warrendnj at gmail.com
Tue Apr 14 09:30:48 CEST 2009

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 two
atoms belonging to two molecules.

Any susggestions on how the pull code can be utilized is very much


On Tue, Apr 14, 2009 at 2:14 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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 restraint
>> between two molecule types in Gromacs?
> Indeed. You will need to create a moleculetype that contains both/all the
> molecules of interest. Note that atom numbers within a moleculetype must be
> unique.
> Mark
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