[gmx-users] forcefield validation
dmobley at gmail.com
Tue Oct 16 18:09:48 CEST 2007
Alan Dodd's suggestion is nice, but there isn't always a lot of
experimental data available for a particular molecule we can compare
with -- or perhaps we want to begin with "good" parameters and then
see if our method can reproduce experiment. Anyway, for whatever
reason it isn't always possible to do the sort of validation he
The other basic approach the field takes is to do the following:
(a) Make sure your molecule of interest can be expected to be
well-described by standard parameterization procedures
(b) Pick the force field you want to use for the rest of your system of interest
(c) Derive parameters for your small molecule using the same procedure
as that used for the force field for the rest of the system (b) to
(d) Assume that the parameters are OK, since they are consistent with
the rest of your force field, and proceed.
Consistency is really the name of the game here when direct comparison
with experiment can't be used for validation. You want to make sure
your parameters are consistent with the rest of the force field which
*has* been validated against experiment. And then, you also assume
that if you follow the procedure that led to that validated force
field, it also should give you good parameters for your small
These are certainly important questions.
With regards to prodrg, at the very least you will need to re-derive
partial charges. But you also need to make sure it is consistent with
the rest of the force field you choose to use, which means you need to
look at those other issues as well. In particular, how is prodrg
deriving parameters? Is the procedure the same as that used for your
force field of interest?
I realize this may all seem like a pain in the neck if you just want
to simulate something. But you can't put garbage/inconsistency in and
expect to get something good out.
On 10/16/07, Qin Shanshan <sansanqin00 at mails.tsinghua.edu.cn> wrote:
> Dear gms-users, I have a fundamental question to put forward. If I want to
> construct a forcefield for an organic molecule of middle size,which has
> about 100 atoms, how can I prove that my forcefield for this molecule is
> correct? Althouth we can get ffgmx itp files from prodrg server, can we be
> sure that these topologies are definitely correct? If we want to convince
> others that our topologies are right, is there any criteria to compare with?
> If I want to derive a forcefield for a particular molecule, what should I
> Any suggestion will be appreciated, thanks very much in advance.
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