Hi all.
Ok, I found the erors. One small in the topology, and another huge in the
.gro formating.
I'll deal with a few other molecules in the next days, and hopefully I'll be
able to make a small contribution to the programs library with a little
"add_dummies" program.
Will test it a bit more, t
Hi all.
Just informing, I tried a single molecule, and the topology with all dummies
minimize (despite taking loads of steps bfgs steps).
The interesting thing is that the distance between atom 6 and 17 at
beggining reads 3.1 angstrons, and at the end read 2.9 angstrons.
Why it's going bad with
Jones de Andrade wrote:
Hi Prof. David.
Yes, it a self created topology. This one is based on another self
created topology that runs perfectly for cyclohexane. It was adapted to
include the dummy atoms.
I guess there is something wrong in the definition of the dummies in the
topology. But
Hi Prof. David.
Yes, it a self created topology. This one is based on another self created
topology that runs perfectly for cyclohexane. It was adapted to include the
dummy atoms.
I guess there is something wrong in the definition of the dummies in the
topology. But I have no clue where it is. Ca
Jones de Andrade wrote:
Hi Prof. David.
What details do you mean? Actual topology files are attached. Anything else?
Thanks a lot in advance!
Sincerally yours,
Jones
There is something wrong in the topology, youäll have to debug it
yourself...
--
David van der Spoel, Ph.D.
Molec. Biophys.
Jones de Andrade wrote:
Hi Prof. David.
What details do you mean? Actual topology files are attached. Anything else?
Is this a topology from pd2gmx or did you write it yourself?
Please check chapter 5 of the manual.
You want to check exclusions ánd start with one molecule.
Thanks a lot in a
Hi Prof. David.
What details do you mean? Actual topology files are attached. Anything else?
Thanks a lot in advance!
Sincerally yours,
Jones
On 10/11/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
>
> Jones de Andrade wrote:
> > Thanks Prof. David.
> >
> > I've done all that now, but at t
Jones de Andrade wrote:
Thanks Prof. David.
I've done all that now, but at the moment I'm locked getting lots of the
"lovelly" error:
Warning: 1-4 interaction between 7 and 16 at distance 4.302 which is
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
Thanks Prof. David.
I've done all that now, but at the moment I'm locked getting lots of the
"lovelly" error:
Warning: 1-4 interaction between 7 and 16 at distance 4.302 which is larger
than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your syste
Jones de Andrade wrote:
Hi all.
Well, I'm having a bit of trouble here because the work has decided to
go in the direction of something I've never used before with gromacs:
dummy atoms (or now "virtual sites").
I assume this is not for a protein, in which case pdb2gmx does it for you.
I've
Hi all.
Well, I'm having a bit of trouble here because the work has decided to go in
the direction of something I've never used before with gromacs: dummy atoms
(or now "virtual sites").
I've got at least three questions in order to use them:
1 - does the virtual sites need to be included in the
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