On 1/31/13 4:10 PM, Matt Watkins wrote:
Oops. Well, I'd be interested in people's opinions and don't intend to hijack
FX's thread.
I do use the code regularly and greatly appreciate all the effort that people
have put into its development. But, particularly, the inability to easily mix
buckingham and lennard-jones is awkward for easily mixing inorganic/organic
systems.
Apologies again to those offended, and maybe it could be a useful discussion,
Feature requests are always welcome on redmine.gromacs.org. In the past 7 or so
years of reading this list, I can count on one hand the amount of times people
have asked about mixing Buckingham and LJ interactions, if that gives you any
idea. Either people who want it are very quiet, or there's not a very
persistent need for such features. The core development team only implements
what they feel is generally useful or has been necessary for their own work.
There is only so much time to get all these things done, and version 4.6 IMHO
represents a heroic amount of effort given all the new toys we have to play
with. If people have useful contributions for various features, they are always
welcome. Gromacs is open-source for a reason :)
Gromacs was indeed built around biomolecular simulations, but I have seen people
do rather elegant and creative work with other systems. Any time I do anything
particularly crafty, I write a tutorial ;) Gromacs is very user-driven.
We are on our way to version 5.0, which will likely represent significant change
to just about everything. If there are features you want (or even better, are
willing to help develop), Redmine is the place to file away wishlists, and the
gmx-developers mailing list is the appropriate forum to talk about code.
-Justin
On Thu, 31 Jan 2013 19:32:36 -0000, FX <fxcoud...@gmail.com> wrote:
Hello,
I'm trying to prepare a MD of a hybrid organic-inorganic crystal, i.e. only
one big molecule extending throughout space with PBC. I have prepared my .gro
file from the PDB (and checked it with babel/vmd). I'm trying to generate the
topology with g_x2top. I have:
- created a directory for my forcefield
- suitable atomname2type.n2t in there
- forcefield.itp file with my bonded forcefield parameters
However, g_x2top complains about not finding the expected number of bonds:
g_x2top -f zif8.gro -o topol.top -ff myff -name test -pbc
Fatal error:
Could only find a forcefield type for 240 out of 276 atoms
The weird part is: all zinc atoms should be equivalent, so there is no reason
for some to have 2 or 3 bonds while the others have 4 (as expected). Given
that the .gro file is correct (including PBC), where could the problem come
from? And how to diagnose it further?
Thanks in advance for any hint, and apologies if I've not given enough
information (or too much).
Sincerely,
FX
PS: I don't know what's the policy on this list, so in doubt I attach the
directory with my files
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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