[AMBER] amber frcmod file

From: Neha Gandhi <n.gandhiau.gmail.com>
Date: Thu, 3 Aug 2017 18:51:40 +1000

Dear List,

I came across paper by Hummer et al wherein they discuss parameters for
carbon nanotube.

"Molecular dynamics simulations were performed at constant pressure24
(1 bar, box length *L* = 32.06 ± 0.04 Å) and temperature (300 K) with AMBER
6.0 (University of California at San Francisco), with particle-mesh Ewald
and cubic-spline interpolation (~1 Å grid width). A time step of 2 fs was
used. Structures were saved every 1 ps. The carbon atoms are modelled as
uncharged Lennard–Jones particles with a cross-section of *σ*CC = 3.400 Å
and a depth of the potential well of *ε*CC = 0.086 kcal mol-1,
corresponding to *sp*2 carbons in the AMBER96 force field26
Carbon–carbon bond lengths of 1.4 Å and bond angles of 120° are maintained
by harmonic potentials with spring constants of 938 kcal mol-1 Å-2 and 126
kcal mol-1 rad-2. In addition, a weak dihedral angle potential is applied
to bonded carbon atoms. The carbon–water Lennard–Jones parameters are *σ*CO
= 3.2751 Å and *ε*CO = 0.114333 kcal mol-1. We also conducted a 25-ns
simulation with modified carbon–water Lennard–Jones interactions of *σ*′CO
= 3.4138 Å and *ε*′CO = 0.06461 kcal mol-1, thus weakening the
water–nanotube van der Waals attractions by a factor of about two"

Based on the above paragraph, I prepared my frcmod file. Can anybody verify
if I have entered correct values? Also how can I modify LJ interactions
between water and nanotube?

CE 12.0

CE-CE 938.0 1.4000

CE-CE-CE 126 120

CE-CE-CE-CE 4 14.50 180.0 2.

  CE 1.7 0.086

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Received on Thu Aug 03 2017 - 02:00:03 PDT
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