Hi everyone,
I have a question about how pmemd handles van der Waals interactions, electrostatic interactions and long-range corrections by default. Here is my input file to pmemd:
&cntrl
imin=0,
ntx=5,
irest=1,
ntxo=2,
ioutfm=1,
ntwv=-1,
iwrap=1,
ntave=10000,
nstlim=1300000,
dt=0.002,
ntf=2,
ntc=2,
temp0=283.15,
ntpr=100,
ntwx=100,
cut=8.0,
ntb=2,
ntp=1,
ntt=3,
gamma_ln=2.0,
ig=-1,
/
I have the following questions about the resulting output:
1. I have chosen for the cutoff distance for nonbonded interactions to be 8 angstroms. Does this apply to both van der Waals and electrostatic interactions?
2. I do not think I have included any keywords that invoke a change to the long-range correction calculation. By default, is there any long-range correction that is applied?
I ask because the AMBER 14 manual states "The Particle Mesh Ewald (PME) method is always "on", unless ntb = 0. PME is a fast implementation of the Ewald summation method for calculating the full electrostatic energy of a unit cell (periodic box) in a macroscopic lattice of repeating images."
Therefore, I want to check that, by default, the PME summation method is performing long-range corrections to electrostatic interactions.
Thank you all for your time.
Best,
Aseel Bala
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Received on Tue Mar 06 2018 - 13:00:02 PST
