[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units
Berk Hess
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)
>reduced units
>Date: Mon, 16 Jul 2007 06:56:41 -0400
>
>Hi guys,
>
>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
steps.
This gives less integration accuracy but can give a lot of "interaction"
accuracy
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
>small.)
>
>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,
>Frankie
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.
Berk.
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