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

From: Ruth Helena Tichauer <rhtichau.laas.fr>
Date: Mon, 24 Sep 2018 22:16:10 +0200

Dear Feng,

Forgive my ignorance but, I’ve checked the manual as you suggested and yet I do not get how to *technically* calculate the average over the initial state. I understand that the exponential of the total work done has to be evaluated in order to get the values of W that dominate the PMF, but then, I don’t know how to calculate the average of this quantities over the initial state.. Could you please point me out some introductory books, lectures, papers, basic examples with which I could fill this knowledge gap I have?

It also says that one should use "different starting coordinates from an equilibrium simulation" hence I suppose the starting structure I have, obtained through a thorough minimisation process, is only useful for a single run, right?

Sincerely,

Ruth

> On 24 Sep 2018, at 17:38, Feng Pan <fpan3.ncsu.edu> wrote:
>
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> Feng Pan
> Ph.D.
> North Carolina State University
> Department of Physics
> Email: fpan3.ncsu.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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Received on Mon Sep 24 2018 - 13:30:03 PDT
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