Hi Stefan and Pär,
I believe that the latest response had the wrong subject, so I am
changing it back.
Pär, two comments:
First, does that option really exist?
$ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z
2>&1; cat z|grep nochargegrp|wc -l
Second, I am not entirely convinced that one can discount the need for
gromacs-style charge groups. When CHARMM includes an atom in the
cutoff, it includes the entire charge group, but that doesn't mean the
algorithms of CHARMM and gromacs are entirely the same, especially
with respect to:
"Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts."
I admit that it has been 3 years since I used CHARMM, but as I recall
the requirement for pair interactions to count within the cutoff is
only that one atom within the charge group is close enough, whereas
the gromacs warning indicates that in gromacs the interaction is only
counted when the center of mass of the charge groups are also within
the cutoff.
Any charmmers out there that can clear this up? I did some searching
on their archives but I was blocked after 3 searches unless I logged
in (ugh!).
I gather that the large charge group listed below is the one that is
spurring the message:
GROUP ! H31
ATOM N NTL -0.60 ! |
ATOM C11 CTL2 -0.10 ! H33-C13-H32
ATOM C12 CTL5 -0.35 ! |
ATOM C13 CTL5 -0.35 ! H21 | H43
ATOM C14 CTL5 -0.35 ! | | |
ATOM H11 HL 0.25 ! H22-C12---N---C14-H42 (+)
ATOM H12 HL 0.25 ! | | |
ATOM H21 HL 0.25 ! H23 | H41
ATOM H22 HL 0.25 ! |
ATOM H23 HL 0.25 ! |
ATOM H31 HL 0.25 ! |
ATOM H32 HL 0.25 ! H11-C11-H12
ATOM H33 HL 0.25 ! |
ATOM H41 HL 0.25 ! |
ATOM H42 HL 0.25 ! |
ATOM H43 HL 0.25 ! |
-- original message --
Hi,
Note, that this is indeed the size of the charge groups in the CHARMM
force field. You could run pdb2gmx -nochargegrp if you know what
you're doing.
Regards,
Pär Bjelkmar
I think the notes from grompp are pretty clear. You need to redivide
your charge groups so that they contain fewer atoms. You can do
this in the .top or .itp file and you can find out how to do that
in the manual. Feel free to post your original and
charge-group-modified topologies back here if you want people to
take a look at them.
Chris.
-- original message --
I am trying to equilibrate a POPC membrane with 128 POPC molecules, but
grompp gives out the following notes and minimization with mdrun does not
work. The output on screen of mdrun comes out like this:
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy = 1.4422483e+17
Maximum force = inf on atom 4082
Norm of force = inf
And grompp notes are:
NOTE 2 [file topol.top, line unknown]:
The largest charge group contains 12 atoms.
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