[gmx-users] modeling cation-pi box

[Justin A. Lemkul]

EGY wrote:
> I am interesting in modeling a small molecule ligand-protein complex that involves a cationic ligand encapsulated by several aromatic residues that form a box around the cation. However, md simulations result in the cation moving outside the box. I am using the CHARMM27 forcefield. Is there a way to restrain the cation portion of the small molecule to within the aromatic box? Or is there a better forcefield, which will take these interactions into consideration.

More than likely you simply need to account for periodicity.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

> Thanks.
> Egy-- 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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