# Re: [AMBER] Fw: Problem Regarding PMF Graph

Date: Fri, 15 May 2015 04:47:22 +0000 (UTC)

Dear Sir,
Thanks for your reply. One thing I could not able to understand why i have to reset the value of pmf is zero around 8 A^0 because

On Monday, May 4, 2015 7:04 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:

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:

> 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
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 ??

Phd Research Scholar
Depeartment of Chemistry
IIT Guwahati

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