Re: [AMBER] Fw: Problem Regarding PMF Graph

From: Adrian Roitberg <>
Date: Mon, 04 May 2015 09:34:52 -0400

The zero in a free energy profile is irrelevant. The only real property
is the free energy difference. WHAM sets the zero of a PMF plot to the
lowest free energy it found, in your case at around ~4 A.

So, to get a negative free energy like you want, you need to reset the
zero in your plot, by hand, to whatever value the PMF has at 8 A

As for the jacobian, it has nothing to do with the zero, but
nevertheless, aqccording to statistical mechanics, you must add that
value by hand yourself.


On 5/4/15 7:34 AM, Shubhadip Das wrote:
> On Monday, May 4, 2015 4:57 PM, 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
>> 12.5A^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
>> but every time
>> minimum value is 0 kcal/mol and in bulk its +ve energy.
>> So i could not able to understand whether i have to do some correction in
>> WHAM code because the
>> minimum value should be around -0.5 to -0.7 at 300K or am i doing
>> something wrong. I have attached my methane-methane PMF curve also.
>> I have found in some paper they have used Alan Grossfield's code to construct PMF
>> but finally they made
>> Jacobian correction {2KTln(r)}. Is it necessary to do this Jacobian
>> correction to get the negative value at minimum position of PMF and 0
>> kcal/mol at bulk i.e i have to subtract the Jacobian term at every
>> position of the graph ??
>> Please advice. Thanks in advance.
>> Shubhadip Das
>> Phd Research Scholar
>> Depeartment of Chemistry
>> IIT Guwahati
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Dr. Adrian E. Roitberg
Department of Chemistry
University of Florida
AMBER mailing list
Received on Mon May 04 2015 - 07:00:02 PDT
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