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

bipin singh bipinelmat at gmail.com
Mon Oct 7 19:39:41 CEST 2013

Thanks for the reply Dr. Justin.
I have also thinking of the same possibility but to further confirm, I am
sending the link for the plot of the distance between the COM of ligand
binding pocket and COM of ligand molecule, please find some time to have a
look at the plot and let me know if it seems a feasible behaviour during a


On Mon, Oct 7, 2013 at 8:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ==============================**====================
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
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Thanks and Regards,
Bipin Singh*

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