[AMBER] Fw: Problem Regarding PMF Graph

From: Shubhadip Das <d.shubhadip.yahoo.com>
Date: Mon, 4 May 2015 11:34:01 +0000 (UTC)

      On Monday, May 4, 2015 4:57 PM, Shubhadip Das <d.shubhadip.yahoo.com> 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
> 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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Received on Mon May 04 2015 - 05:00:02 PDT
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