[gmx-users] g_x2top is missing bonds
jalemkul at vt.edu
Thu Jan 31 22:54:33 CET 2013
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
> 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.
> On Thu, 31 Jan 2013 19:32:36 -0000, FX <fxcoudert at gmail.com> wrote:
>> 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).
>> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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