Re: [AMBER] Fw: Problem Regarding PMF Graph

From: Shubhadip Das <>
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
                my system's half box length is around 12.4 A^0. Please advice. Thanks in advance.

     On Monday, May 4, 2015 7:04 PM, Adrian Roitberg <> 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:
       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
  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

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
AMBER mailing list
Dr. Adrian E. Roitberg
Department of Chemistry
University of Florida

AMBER mailing list
Received on Thu May 14 2015 - 22:00:02 PDT
Custom Search