[gmx-users] Tolerance and damping coefficient

[Justin Lemkul]

On 9/11/18 11:09 AM, Gonzalez Fernandez, Cristina wrote:
> Dear Gromacs users,
>
>
> I am trying to reproduce the simulation of a published article and in it the authors used Particle Meah Ewald for electrostatic interactions with a relative tolerance of 10^⁻6. I have checked the manual and I only have found tolerance parameters for energy minimization, neighbour searching and shake algorithm. Does anyone know how to implement the tolerance for PME?. On the other hand, in the paper Langevin dynamics for temperature and piston

See "ewald-rtol" 
(http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#ewald)

> fluctuations are considered, with a damping coefficient of 1 ps^-1. However, in the Gromacs manual Langevin dynamics only includes bd-fric and ld-seed, whose units differ from ps^⁻1. How can I consider the damping coefficent?

That's tau-t when the integrator is sd (see entry for "sd" in 
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#run-control)

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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