# Re: [AMBER] SMD free energy inferred from work

From: Feng Pan <fpan3.ncsu.edu>
Date: Mon, 24 Sep 2018 11:38:09 -0400

Hi, Ruth

It is not the arithmetic mean, you should use Jarzynski relationship, check
the equation (21.16)
in the manual section 21.7.
For the number of trajectories, it relates with your system and reaction
coordinate, I would recommend
you do 100 first, check if the distribution is good? Then decide if more is
needed.

Best
Feng

On Mon, Sep 24, 2018 at 9:47 AM Ruth Helena Tichauer <rhtichau.laas.fr>
wrote:

> Dear Amber users and developers,
>
> I’m running SMD to evaluate the PMF of a reaction using the following
> input file:
>
> SMD: LCOD rxn coord
> &cntrl
> imin=0,
> irest=1, ntx=5,
> ntb=2, pres0=1.0, ntp=1, taup=1.0,
> cut=12.0,
> tempi=300.0, temp0=300.0,
> ntt=3, gamma_ln=2.0, ig=-1,
> nstlim=20000, dt=0.001,
> ntpr=20, ntwx=20, ntwr=5000, ioutfm=1,
> ntc=2, ntf=2,
> ifqnt=1, infe=1
> /
> &qmmm
> qmcharge=0,
> qm_theory='PM6',
> qmshake=0,
> qmcut=8.0,
> /
> &smd
> output_file = 'nat_smd25-7.txt'
> output_freq = 20
> cv_file='cv_nat-7.in'
> /
>
> And the cv_file:
>
> &colvar
> cv_type = 'LCOD'
> cv_ni=4, cv_i = 2947,2647,2650,2647,
> cv_nr=2, cv_r = 1.0,-1.0,
> npath=2, path = 2.26718,-1.9,
> nharm=1, harm = 25.0
> /
>
> I wonder which is the minimum number of trajectories that I should run and
> how to evaluate the PMF (is it just the arithmetic mean of all the values
> obtained for the total work done?).
>
> Thank you in advance for any insight,
>
> Sincerely,
>
> Ruth
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>

--
Feng Pan
Ph.D.
North Carolina State University
Department of Physics
Email:  fpan3.ncsu.edu
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Received on Mon Sep 24 2018 - 09:00:03 PDT
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