[gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box

[Justin Lemkul]

On 10/7/13 10:46 AM, bipin singh wrote:
> Hello All,
>
> I have calculated the distance between the binding pocket of protein and
> the ligand molecule but due to ligand diffusion out of box, I am getting
> wrong distance as first it increases till 5nm and then decrease again to
> around 1nm during the simulation (which is not possible).
>
> I have fitted my trajectory with using trjconv -pbc mol -ur compact -center
> (protein) option.
>
> I have also tried the -nojump option but getting the same results for
> distances.
>
> Please suggest how to get the real distance without the PBC effect.
>

It sounds like that very well could be the real distance.  If the ligand 
diffused out, it simply becomes part of the solvent around the protein and can 
diffuse around freely.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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