From: "Frankie Montenegro" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: gmx-users <gmx-users@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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