[gmx-users] constraining multiple types of bonds

[tarak karmakar]

thanks a lot Justin
I'll try to follow this protocol.

On Sun, Nov 11, 2012 at 8:59 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/10/12 10:27 PM, tarak karmakar wrote:
>>
>> Thanks Justin
>>
>> If I want to constrain all the bonds in the substrate molecule present
>> inside the enzyme cavity then along with SHAKE what I need to use ?
>>
>
> Set "constraints = none" in the .mdp file and add an explicit [constraints]
> section in the ligand topology.
>
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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-- 
Tarak