On Mon, Oct 17, 2016 at 6:22 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi Hai,
>
>
> Thank you so much for your response.
>
> I have checked, everything seems to be overlapping correctly.
>
>
> Can you explain me what do you mean by
>
> 1. compare PMF 1st and 2nd half of your data
>
>
Split each of the trajectory into two parts, use 1st part for PMF
calculation, do the same thing for 2nd part, then compare two PMFs.
something like:
https://sites.google.com/site/wangtingpage/_/rsrc/1472769957930/home/tutorials/pmf/pmf_18.png?height=296&width=400
Hai
>
>
> Thanking you,
>
> Abhishek
>
> ________________________________
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Monday, October 17, 2016 10:45:31 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] WHAM analysis
>
> On Mon, Oct 17, 2016 at 5:20 PM, Thakur, Abhishek <axt651.miami.edu>
> wrote:
>
> > Hi everone,
> >
> > While doing WHAM analysis my free energy keep on changing with tolerance.
> >
> > When I am using 0.001 tolerance it is 25Kcal/mol
> >
> > II I am using 0.0001 it is around 35Kcal/mol.
> >
> >
> > I am unable to get which value to trust.
> >
>
> May be neither of the energies are trustful due to the convergent issue.
> may be you can try:
> 1. compare PMF 1st and 2nd half of your data
> 2. check energy histogram overlapping:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.
> org_tutorials_advanced_tutorial17_section2.htm&d=DQICAg&c=y2w-uYmhgFWijp_
> IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=9NQEh4bfn6QaBk107i6iftIhjtQ5GB
> uqkwFmgwqxrBQ&s=p8QsX8HL5wXrIY92sbo6CbjSrUtA78GXAMPIFtHsOVw&e=
> 3. run multiple runs and repeat 1, 2
> 4. may be check previous publications about checking convergence.
>
> Hai
>
>
>
> >
> > Any suggestion will be highly appreciated.
> >
> >
> >
> > thanking you,
> >
> > Abhsihek
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Received on Mon Oct 17 2016 - 15:30:03 PDT
