>
>
> Message: 7
> Date: Mon, 25 Jul 2016 16:00:26 +0900
> From: bharat gupta <bharat.85.monu.gmail.com>
> Subject: Re: [AMBER] Steered Molecular Dynamics
> To: amber.ambermd.org
> Message-ID:
> <CAAh+zSXwkK8qzWyo7gHs8EZnE=
> z-y0GB0p2UeOxVoou6nE46pA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello Amber Users,
>
> Can anybody explain me the meaning of the following input file used for a
> SMD run?
>
> #Reaction coordinate
> #Dist H3OH-Os, Os-S, S-N y HN-Owat
> &rst iat=4536,3483,3483,3482,3482,3487,3488,19505, rstwt=-1,1,-1,-1,
> r2=-6.09, rk2=200, r2a=-2.0, /
>
> H3OH-Os, Os-S, HN-Owat : involves bond break and atom transfer
> S-N : involves bond formation
>
>
>
> --
> *Best Regards*
> BM
>
>
> ------------------------------
>
> Message: 8
> Date: Mon, 25 Jul 2016 09:06:11 +0200
> From: Adrian Roitberg <roitberg.ufl.edu>
> Subject: Re: [AMBER] Steered Molecular Dynamics
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <379a456b-d631-3930-8a6f-76b77a170067.ufl.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> There will be a harmonic restraint applied to a reaction coordinate. The
> force constant will be 200 (kcal/mol)/A^2 and the center of the
> restraint will move from -6.09 to -2.0 in nstlim steps (nstlim is in the
> main namelist)
>
> The reaction coordinate is defined as the sums and differences between
> FOUR distances.
> RC = -d1 + d2 - d3 -d4
>
> d1 = distance between atoms 4536 and 3483
> d2 = distance between atoms 3483 and 3482
> d3 = distance between atoms 3482 and 3487
> d4 = distance between atoms 3488 and 19505
>
> Is this clear ?
> adrian
>
> > Hello Amber Users,
> >
> > Can anybody explain me the meaning of the following input file used for a
> > SMD run?
> >
> > #Reaction coordinate
> > #Dist H3OH-Os, Os-S, S-N y HN-Owat
> > &rst iat=4536,3483,3483,3482,3482,3487,3488,19505, rstwt=-1,1,-1,-1,
> > r2=-6.09, rk2=200, r2a=-2.0, /
> >
> > H3OH-Os, Os-S, HN-Owat : involves bond break and atom transfer
> > S-N : involves bond formation
> >
> >
> >
>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
>
Dear Prof. Roitberg,
Thank you for your response. I understood from your explanation that the
numbers represent the reaction coordinate as the sum and difference between
a set of 4 atoms. Could you please tell me, for instance, if I want to make
a S-N bond (atom no. 3482, 3487) when the original distance between these
two atoms is around 3.5 Angstrom, what should be the value for r2 and r2a?
I can very well understand the values for r2 and r2a if there is a single
reaction coordinate, for eg, as given in this tutorial:
http://ambermd.org/tutorials/advanced/tutorial26/section2.html. But, I am
unable to decide how to provide values for r2 and r2a, particularly when
there are 3 or 4 reaction coordinates, which involves bond break or proton
transfer?
Since, I am studying a similar where there is a simultaneous bond break and
proton transfer, it is very important for me to understand how to set r2
and r2a in cases where there are more than 3 reaction coordinates. I would
be highly obliged if you could respond to my query.
--
*Best Regards*
Bharat
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 25 2016 - 22:30:02 PDT
