Re: free energy changes via FEP method

From: Brian Radak (bradak_at_anl.gov)
Date: Wed Dec 16 2015 - 12:15:10 CST

My guess is that your first thought is correct - the simulations are not
long enough.

I would recommend:

1) assessing the statistical error (I'm not really familiar with
ParseFEP, so I don't know if it does this already)

and/or

2) trying another analysis method (such as a multistate technique)

HTH,
Brian

On 12/15/2015 09:59 AM, Haleh a wrote:
> Dear NAMD users,
>
> I have been trying to calculate free energy changes upon a mutation in
> a protein via FEP method. The transformations were subdivided into 32
> windows. Each stratum consisted of 100,000 data-collection steps
> preceded by 25,000 equilibration steps.
> For a few of my mutations the free energy change upon forward and
> backward transformations were not the same. An example of a Parsefep
> file for dG column is given below:
>
> fwbw
> 0.000019.2024
> 7.859727.3887
> 15.858535.4349
> 23.835042.7734
> 30.986949.8046
> 38.143356.4785
> 45.132663.2339
> 51.556469.8128
> 57.979575.7305
> 64.268181.6443
> 70.273286.9015
> 76.054791.6371
> 81.094195.7292
> 85.202199.6043
> 88.3743103.2919
> 91.4066106.3001
> 93.3668108.3961
> 91.4244106.6218
> 89.3347104.5966
> 87.0627101.5024
> 84.633097.8175
> 81.776693.0725
> 78.847388.2228
> 75.564583.1926
> 70.459677.7998
> 65.076071.9186
> 59.682565.5346
> 54.129159.0037
> 48.544652.6676
> 42.786345.8779
> 36.926138.9123
> 31.023131.7249
> 25.144525.1445
>
>
> I tried running the simulation with longer data collection and
> equilibration time but it did not help. Does anyone have any idea why
> such a problem exist and how to solve it?
>
> Many thanks,
> Haleh Abdizadeh

-- 
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak_at_anl.gov

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