On Fri, Aug 14, 2009 at 10:50:29AM +0200, Berk Hess wrote:
>
> Hi,
>
> For systems with vacuum the automatic domain decomposition setup does
> not do a good job. It currently decomposes based on the box dimensions,
> not on the actual atom distribution in the box.
> I was thinking of improving th
is running on 8 cores
of a single machine.
I would appreciate suggestions,
Borys Szefczyk
--
REQUIMTE, & Molecular Modelling & Quantum Chemistry Group,
Department of Chemistry, & Institute of Physical & Theoretical Chemistry,
Faculty of Scie
On Sun, Jun 07, 2009 at 05:35:14PM +0200, Florian Dommert wrote:
> Glad to hear the my help works. Setting the LJ parameters zero for the
> should avoid a further contribution of the LJ part from the defined 1-5
> IA, since they are already present in the nonbonded part of the
> interaction types.
On Sat, Jun 06, 2009 at 02:06:56PM +0200, Florian Dommert wrote:
> * David van der Spoel [2009-06-06 08:06:26 +0200]:
>> The VDW may work, but not differently scaled 1-4 and 1-5 coulomb
>> interactions.
>
> Where is the matter if I have a [ pairs ] directive in the itp file like
> this :
>
>
>
On Fri, Jun 05, 2009 at 10:31:22AM +1000, Mark Abraham wrote:
> Setting the number of exclusions for a moleculetype to 4, in a forcefield
> with "generate_pairs = yes" and "fudgeLJ = 0.5" will probably see pdb2gmx
> get everything except the 1-5 interactions right. Then you post-process the
> .t
there a way to
do this within the topology file of Gromacs or do I need to modify the code?
Regards,
Borys Szefczyk
--
REQUIMTE, & Molecular Modelling & Quantum Chemistry Group,
Department of Chemistry, & Institute of Physical & Theoretical Chemistry,
erse order, first CL, then NA, I get:
D[ CL-] = 6.4607e-5 cm^2/s
D[ NA+] = 4.2326e-5 cm^2/s
Again, first plot look fine, the second - not.
Why these results differ?
Regards,
Borys Szefczyk
--
REQUIMTE, & Molecular Modelling & Quantum Chemistry Group,
Depar
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