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
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=9NQEh4bfn6QaBk107i6iftIhjtQ5GBuqkwFmgwqxrBQ&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 - 15:30:02 PDT
