# Re: [AMBER] Reaction Coordinate that is the Difference of two Distances

From: <diego.soler.uam.es>
Date: Wed, 14 Mar 2018 17:19:21 +0100

Thank you, Ruth!

Actually, I have also been able to achieve it by writing a restraint
file of the form:

&rst iat=1,4,4,21,,
iresid=0, ifvari=1,nstep1=0, nstep2=1000,
rstwt=1,-1
r1=-10.000, r2=-1.2000, r3=-0.8000, r4=10,
r1a=-10.000, r2a=1.0000, r3a=1.0000, r4a=10,
rk2=500, rk3=500,rk2a=2000, rk3a=2000,
&end

In the first line I indicate the atoms involved in the colective
variable and the rstw is the set of weights for each distance.

Sincerely,
Diego SP

Quoting Ruth Helena Tichauer <rhtichau.laas.fr>:

> Dear Diego,
>
> If I understand well what youâ€™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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>
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Received on Wed Mar 14 2018 - 09:30:02 PDT
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