Gavin Melaugh wrote:
I hope this doesn't come across as stupid, or worse insolent. But what
is the point in stating the charges in the atom type section then ?
They're probably a holdover from some earlier Gromacs version (an ancient one)
that used those charges somehow, or they were listed there as some grand idea to
have a more universal, streamlined topology builder that could use generic
charges. Just a guess. They stayed there because it's far easier to just
ignore the unnecessary information than the re-write the code and those files
such that the lines are read properly with one less field. The charges can be
useful for starting parameterization; they are based on common functional groups
that may not be far off from the correct values in many cases.
-Justin
Gavin
Mark Abraham wrote:
On 02/08/11, *Gavin Melaugh * <gmelaug...@qub.ac.uk> wrote:
Hi Justin
I see that we may have got our wires crossed from the off.
Consider the [pairs] directive, which determines which atoms interact
in a 1,4 manner. Consider two atoms listed the [pairs] directive. From
the point of the Coulombic interaction between these two atoms I suppose
my original question should have been: Does mdrun, when calculating the
Coulombic potential between these two atoms, use the charges assigned to
the atoms in the [atomtypes] directive or [atoms] directive ?
The charges from [atoms] are used. The charges in [atomtypes] are
never used in any forcefield currently used with GROMACS. It might not
be possible for grompp to ever use them, but I'd have to check the
code for that.
Mark
Cheers
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Yes I think the example vindicates what I am saying as well. I
suppose I
the "contradiction" ( I'll call it the point of confusion) you
refer to
is perhaps when Justin (who is always more than helpful) said that
"Charges are irrelevant for generation of pair interactions.
Nonbonded
pair interactions are LJ, not Coulombic. You will certainly have 1-4
Coulombic interactions, but they are not generated by gen_pairs. See
manual section 5.3.4."
Charges *are* irrelevant - the information is not used when generating
pairs, which I thought was the original question. The charge
information is used during MD, when the pair list tells mdrun which
atoms interact in what way. Then you get Coul. 1-4 terms. Perhaps I
missed your point, but this whole thread started as "which charge is
used to generate pairs?" The answer is still none.
My sequence of 1-4 interaction generation should go like this I
suppose:
e.g.
[pairs]
3 6
no parameters present therefore get from [pairtypes] directive.
no [pairtypes] directive therefore get from [non_bonded parameters]
directive as gen pairs = yes
again no [non_bonded parameters] directive.
Therefore generate 1,4 interaction parameters based on the normal
sigma
and epsilon values (comb rule 3) present in [atomtypes] directive, in
accordance with fudge LJ and QQ.
My point is, then in conclusion, that in this way surely the 1,4
electrostatic interactions are determined by the pair list and in my
case gen_pairs = yes.... no?
Yes.
-Justin
Many Thanks
Gavin
Mark Abraham wrote:
On 02/08/11, *Gavin Melaugh * <gmelaug...@qub.ac.uk> wrote:
Hi Mark
Thanks for the reply.
I am currently reading that section of the manual and, unless I am
completely mistaken, it seems to vindicate what I am saying.
"Extra Lennard-Jones and electrostatic interactions between pairs of
atoms in a molecule can be added in the [pairs] section of a
molecule
definition".
In my [atom types] directive I have atomtype, charge mass, sigma and
epsilon etc. All nonbonding parameters are then calculated
according to
the combination rule (in my case 3). 1-4 interactions are then
calculated based on the information in [pairs] directive (all atoms
are
three bond away). I just have the atom indices of each pair in this
directive therefore with gen_pairs = yes, the interaction parameters
between each pair (which are 1-4) are calculated based on Fudge
LJ and
Fudge QQ (which are both 0.5 in my case). All of this in conjunction
with nrexcl =3.
That will generate parameters for the interactions listed in [pairs]
that do not have corresponding [pairtypes]. FudgeLJ and
[nonbond_params] are used in such generation, per other parts of 5.7.
Or am I completely wrong?
In my set up then, are 1-4 Coulombic interactions determined by the
pair
list and fudge QQ?
If the contradiction you think exists is this one...
On 02/08/11, *Gavin Melaugh * <gmelaug...@qub.ac.uk> wrote:
Hi Justin
Again thanks for the reply. I am not disagreeing with you but If I
don't
include a [pairs] directive in the topology file (with gen_pairs
=yes),
then there are no 1-4 LJ nor 1-4 Coulombic energies written in
the log
file. When I include the [pair s] directive then both types of
interaction are written to the log file. Therefore does gen_pairs=
yes +
[pairs] directive generate 1,4 LJ and 1,4 Coulomb according to
fudge LJ
and QQ?
... then 5.3.4 indicates that the presence of a [pairs] directive
will
generate the 1,4 output fields. The parameters for that output are
taken from [pairtypes]. If gen-pairs=yes then the parameters are
generated, else some warning/error occurs. The example in 5.7.1 has
some more explanation about the use of the fudge parameters.
Mark
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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