Maybe try using VFEP From Darrin York's group, developed by Taisung Lee
.
https://sites.google.com/site/cancersimulation/software
This software has been good to us in some occasions.
On 8/20/16 2:13 PM, Chi Jin wrote:
> Hi, Amy,
>
> I guess there should not be "edges" in my PMF plot since my system is consist of two dihedrals and I turned on periodicity to both two dihedrals.
>
> Attached is the overlapping of the windows along the two dihedrals along with the final results. When running this, I set all the force constants of all constraints in the metadata file to 0.06092 (meaning 100 kcal/mol/degree in Amber) just for test to avoid mistyping the force constants. The command line was:
> ./wham-2d Px -180 180 120 Py -180 180 120 0.0001 300 0 metadata result 0 >out
> The final result looks weird. When I switched to use the metadata containing the real force constants, I got similar results.
>
> Thank you for reply!
>
> ________________________________________
> From: Amy Rice <arice3.hawk.iit.edu>
> Sent: Saturday, August 20, 2016 11:41 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] WHAM analysis
>
> Hi Abhishek,
> There is not nearly enough information in your original email to let us
> help you. Some information that would be useful to provide- What is your
> reaction coordinate? How long is your simulation? Are you seeing sampling
> in each bin?
>
> Jin Chi- is the surface discontinuous when you plot it? It's hard to see
> from the portion of the WHAM output that you provided, but since this is a
> 2D PMF, these infinite values could represent an edge and not necessarily a
> discontinuity or hole in the PMF.
>
> Hope this helps,
> - Amy
>
> On Sat, Aug 20, 2016 at 2:30 AM, Chi Jin <jinchi.chemistry.msu.edu> wrote:
>
>> Me too. I ran wham-2d, the 4th column is the unnormalized probabilities:
>>
>> 118.500000 127.500000 7.185208 2.608360
>> 118.500000 130.500000 6.997535 3.575855
>> 118.500000 133.500000 7.204882 2.523505
>> 118.500000 136.500000 6.304755 11.459057
>> 118.500000 139.500000 inf 0.000000
>> 118.500000 142.500000 inf 0.000000
>> 118.500000 145.500000 inf 0.000000
>> 118.500000 148.500000 6.228352 13.029487
>> 118.500000 151.500000 6.640700 6.514633
>> 118.500000 154.500000 5.443592 48.735702
>> 118.500000 157.500000 inf 0.000000
>> 118.500000 160.500000 4.994485 103.686285
>>
>> So that the PMF surface is not continuous, which doesn't sound reasonable
>> to me.
>> Jin Chi
>> PhD student
>> Department of Chemistry
>> Michigan State University
>> East Lansing, MI 48824
>> Tel: (517)-355-9715 x261
>> jinchi.chemistry.msu.edu
>>
>> ________________________________________
>> From: Thakur, Abhishek <axt651.miami.edu>
>> Sent: Friday, August 19, 2016 5:55 PM
>> To: amber.ambermd.org
>> Subject: [AMBER] WHAM analysis
>>
>> Hi
>>
>> I am trying to do WHAM analysis after QM/MM.
>>
>> But the result file that I am getting is [😎]
>>
>> #Coor Free
>> 3.471739 0.221101
>> 3.615217 inf
>> 3.758696 inf
>> 3.902174 inf
>> 4.045652 inf
>> 4.189130 1.645569
>> 4.332609 0.000000
>> 4.476087 inf
>> 4.619565 inf
>> 4.763043 inf
>> 4.906522 inf
>> 5.050000 2.616324
>> 5.193478 0.022866
>> 5.336957 2.745523
>> 5.480435 inf
>> 5.623913 inf
>> 5.767391 inf
>>
>>
>> Now I don't know why this inf is coming in my result file.
>>
>>
>> Thanking you,
>>
>> Abhishek
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> Amy Rice
> Ph.D. Student
> Physics Department
> Illinois Institute of Technology
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Sat Aug 20 2016 - 11:30:03 PDT
