[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units
gmx3 at hotmail.com
Mon Jul 16 14:17:12 CEST 2007
>From: "Frankie Montenegro" <frankie.montenegro at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users <gmx-users at gromacs.org>
>Subject: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion,and b)
>Date: Mon, 16 Jul 2007 06:56:41 -0400
>My first question is with regards to the size relationship
>between rlist and rvdw/rcoulomb, and consequently the
>meaning of rlist.
There are three options in Gromacs.
The option you want is rcoulomb < rlist and rvdw < rlist.
This works and gives the most accurate and also the most costly integration.
A faster and very commonly used setting is: rlist=rcoulomb=rvdw.
With PME the Coulomb interactions are very small at the cut-off,
as are the LJ interactions.
So with a small sacrifice in integration accuracy one can gain a lot
of performance, also because analytical LJ is cheaper than tabulated.
The last option is rcoulomb > rlist and/or rvdw > rlist.
Then the energies and forces beyond rlist are only updated every nslist
This gives less integration accuracy but can give a lot of "interaction"
at a small computational cost.
>My second question
>I am trying to minimize a model binary Lennard-Jones system.
>It is a cubic box, side length 5 sigmas (so, the size is in
>reduced units, sigma=1).I have two atom types, so I followed
>the manual and set sigma_ii = epsilon_ii = 1 for one atom type.
>I set rlist=1, but grompp_d complaines that
> "ERROR: The cut-off length is longer than half
> the shortest box vector or longer than the
> smallest box diagonal element. Increase the
> box size or decrease rlist."
>Now, it seems to me that, if sigma_ii = 1, all lengths values in the
>mdp file (such as rlist) will be in units of sigma. Am I right
>here? r*=r/sigma=r/1=r, right? If so, why is grompp complaining about
>the size which is less then a quarter of the
>box? (At first I thought it is complaining about rlist being too
>So, in conclusion, I either don't understand:
>A) meaning of the size of rlist,
>B) conversion to reduced units,
>C) quite possibly both.
>Here is my potential, if that can be of any help.
>PE_ij=sigma_ij^6 * [ 16.0* epsilon_ij / R_ij^6
> - 12.0 * epsilon_ij * r_ij^2 / R_ij^8
> - 4.0 * epsilon_ij / r_ij^6 ]
> +sigma_ij^12 * [-28.0 * epsilon_ij / R_ij^12
> +24.0*epsilon_ij * r_ij ^2/ R_ij^14
> + 4.0 * epsilon_ij / r_ij^12 ]
>where R_ij= const * sigma_ij
>is the cutoff for each of the three interactions.
>Thanks for your help,
In Gromacs the units that you put in are the units you get out.
The only exceptions are temperature, which involves the Boltzmann constant
and pressure, which involves a factor of 16.6.
So if you box size is 5 (as you say) and your cut-off is 1, then you
should not get an error.
So one of the two things is wrong.
Maybe you made a pdb file with box 5?
pdb is in Angstrom, while Gromacs uses nm, so there is a conversion
factor of 0.1.
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