Did you include the -2kTln r Jacobian correction?
Cheers,
Brian
On 04/19/2015 10:49 AM, Shubhadip Das wrote:
> > Dear users,
>> I am new in umbrella sampling.
>> I am doing umbrella sampling in AMBER12 and to construct PMF i have used
>> WHAM. As i am new in this so first i have tried with known simple methane molecules.
>> I have used 10 methane molecules and 490 water molecules.
>> I have used 5 starting structure 12.5, 10.5, 8.5, 6.5, and 4.5A^0.
>> The umbrella sampling was conducted for 3.0 A^0 to 12.5 A^0 which
>> was divided into 39 bins with window lengths of 0.25 A^0 Using
>> K=4kcal/mol/A^0^2. I run each an every simulation upto 2ns (production run) and i have
>> checked that windows have overlap properly. And next to run WHAM i have
>> used the following command
>> wham 2.9 12.6 39 0.01 298 0 meta.dat results.dat
>> My inputs files for restrain are given below
>>
>>
>> Harmonic restraints for 10 ang
> &rst
> iat=1,4,
> r1=0.0, r2=10.0, r3=10.0, r4=99.0,
> rk2=4.0, rk3=4.0,
> /
>> I have only change the r2 and r3 for different simulation from 3A^0 to 12A^0.
>>
>> But the pmf graph is not matching with standard methane pmf graph. I have used smith model
>> for methane molecule and SPC/E water model. Minimum is coming around 3.8 A^0 but the minimum
>> value is 0 kcal/mol. and also at half box length its not going to 0 kcal/mol i.e its giving
>> +ve free energy. I have checked with different different force constant value but every time
>> minimum value is 0 kcal/mol and in bulk its +ve energy.
>> So i could not able to understand wheather i have to do some scaling in WHAM code because the
>> minmum value should be around -0.5 to -0.7 at 300K or am i doing something wrong.
>> Please advice. Thanks in advance
>> Shubhadip Das
>> Phd Research Scholar
>> Depeartment of Chemistry
>> IIT Guwahati
>
>
>
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--
Brian Radak
Postdoctoral Scholar
Gordon Center for Integrative Science, W323A
Department of Biochemistry & Molecular Biology
University of Chicago
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
email: radak.uchicago.edu
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Received on Thu Apr 23 2015 - 06:30:02 PDT
