[gmx-users] A questin to Justin on methods in the PPARγ-RXRα-DNA complex paper

Timofey Tyugashev tyugashev at niboch.nsc.ru
Sat Feb 20 07:56:47 CET 2016

I was looking for examples of calculation setups. So I have a couple of 
questions about one used in this paper 
Parameters are amber99sb-ildn and gaff:
"Simulations were carried out with GROMACS [40,41], version 4.6. All 
bonds were con-
strained using the P-LINCS algorithm [42], allowing an integration time 
step of 2 fs. The Verlet
cutoff scheme [43] was used with a minimum cutoff of 1.0 nm for 
short-range Lennard-Jones
interactions and the real-space contribution to the smooth Particle Mesh 
Ewald algorithm
Why all-bonds constraints are applied? Isn't AMBER FF are supposed to be 
used with h-bond constraints? Is there any notable difference between 1 
and 2fs timestep in this setup?
Is box-solute distance of 1.0nm sufficient for 1.0nm LJ cuttof?
And why run three independent 500ns simulations instead of one or two of 
longer duration? Only to check for reproducibility or are there any 
additional reasons?

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