[AMBER] problem w/ radial results

From: E. Nihal Korkmaz <enihalkorkmaz.gmail.com>
Date: Wed, 22 Aug 2012 16:23:04 -0500

I have an explicit solvent simulation with 0.2 M salt. I am calculating the
gofr of Cl- ions around the protein with the following command in ptraj:

radial distCl 0.05 10 :Cl- :1-93 closest

I am having results that do not make sense, the ions start to line up at
around 0.175 A which is considerably lower than a H--Cl bond length. I
checked the energy values to see if the atoms somehow clash, I found
nothing indicative of that kind. I checked the trajectory in VMD, nothing
looks like .175 A close.

How can I fix that issue?


Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone:  608-265-3644
Email:   korkmaz.wisc.edu

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Received on Wed Aug 22 2012 - 14:30:04 PDT
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