[gmx-users] simulation with ligand at the active site

[onetwo]

Hello Users,

I have a query regarding simulation with the ligand.

In my protein there are two ligands, one of them (coenzyme) is from the
crystal data, and other I have docked at the active site, while docking
it is showing good interaction with all the active site residues very
well.
I used GROMOS96 43a1 force field, and got the topology file made from
prodrg beta, using GROMOS 96.1 for both the ligands.
while doing equilibration I did, brendenson coupling on like
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300

and in MD simulation also
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300

But after 1ns equibiration, one of the ligand (the one which I docked)
is going away from the active site and then I ran it for 4 ns further,
it has gone more far from the cavity. Following is the link to the snapshot of the ligand at different time. 

https://picasaweb.google.com/118389174994698260649/Md_complex?authkey=Gv1sRgCMis2qry3cGj7AE#5600499037480314402

I want to ask if the change in the
position of ligand is justified with the parameters i have taken or it
if i have done something wrong?

Thanks and Regards
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