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From: Jason Swails <jason.swails.gmail.com>

Date: Tue, 1 Oct 2013 12:20:29 -0400

On Tue, Oct 1, 2013 at 9:11 AM, Mohan Pradhan <pradhanmohan56.gmail.com>wrote:

*> Thanks for the suggestions Jason. But I reconfirmed that I have not
*

*> reversed the X-axes. When I plot the dihedral angles sampled from the 2
*

*> simulations (plots attached), I also see less sampling around the dihedral
*

*> angles which correspond to the barriers in those PMF plots.
*

*>
*

These two plots show the same information as the original two. I can think

of only two possible explanations:

1) You are not performing equilibrium sampling because your simulations are

too short and the snapshots are biased by the configurations generated

while relaxing to the 'new' location of the biasing potential (I say 'new'

since I assume you take the final snapshot of the previous window as the

starting coordinate for the next one).

2) You have somehow incorporated a 180 degree phase shift into your

measurement of the dihedral angles. This is deceptively easy to do given

the periodicity of torsion angles.

HTH,

Jason

Date: Tue, 1 Oct 2013 12:20:29 -0400

On Tue, Oct 1, 2013 at 9:11 AM, Mohan Pradhan <pradhanmohan56.gmail.com>wrote:

These two plots show the same information as the original two. I can think

of only two possible explanations:

1) You are not performing equilibrium sampling because your simulations are

too short and the snapshots are biased by the configurations generated

while relaxing to the 'new' location of the biasing potential (I say 'new'

since I assume you take the final snapshot of the previous window as the

starting coordinate for the next one).

2) You have somehow incorporated a 180 degree phase shift into your

measurement of the dihedral angles. This is deceptively easy to do given

the periodicity of torsion angles.

HTH,

Jason

-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Oct 01 2013 - 09:30:08 PDT

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