Dear Diego,
If I understand well what you’d like to do, I would suggest Steered Molecular Dynamics (SMD) simulations. Here is an old post from the mailing list on how to implement it:
http://archive.ambermd.org/201611/0326.html <
http://archive.ambermd.org/201611/0326.html>
All the best,
Ruth
> On 14 Mar 2018, at 16:24, diego.soler.uam.es wrote:
>
>
> Dear all,
>
> I want to perform Umbrella Sampling simulations and Steered Molecular
> Dynamics with a reaction coordinate that is a combination of two
> distances, d1 & d2. d1 is the distance form one atom to another, and
> d2 is another distance between another pair of atoms, and the reaction
> coordinate that I want to use is d2-d2. Is this possible? How can I
> achieve this?
>
> The restriction files I am using look like
>
> &rst iat=6,6,
> iresid=1, ifvari=1,nstep1=0, nstep2=1000,
> atnam(1)='N1', atnam(2)='H1'
> r1=0.000, r2=0.9000, r3=1.1000, r4=10,
> r1a=0.000, r2a=0.900, r3a=0.900, r4a=10,
> rk2=500, rk3=500,rk2a=2000, rk3a=2000,
> &end
>
> Here there is just one distance (from the atom N1 to the atom H1). I
> know I can add as many restrictions of this sort as I want, but I want
> a single restriction (that is, a single harmonic/umbrella potential)
> over a single coordinate that is d2-d1.
>
> Thank you for your help!
>
> Diego SP
>
>
>
>
>
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Received on Wed Mar 14 2018 - 09:00:01 PDT
