Hi,
Yes, this was done on purpose to reflect the different use of charge
groups in CHARMM and GROMACS. Check out the mailing list archives for
more details about this.
On another note you might like to take a look at the contributed
CHARMM36 force field (available to download on the GROMACS website).
There is a DPPG entry in the lipids.rtp file that should help in making
a CHARMM27 DPPG rtp entry (if you wish to use the CHARMM27 lipids rather
than the CHARMM36 ones).
Cheers
Tom
On 06/08/11 00:22, Michael McGovern wrote:
Hi, I'm making a lipid topology for DPPG in the charmm forcefield in
gromacs 4.5. I'm putting it together from pieces of what already
exists as suggested in the charmm files. I noticed that there are
charge groups in the original charmm files, and these were reflected
in the gromacs topology in the 4.5 beta release, but in 4.5.3 and
4.5.4, every atom has its own charge group.
So for instace, POPC in the beta release had a topology that began:
[ POPC ]
[ atoms ]
N NTL -0.60 0
C11 CTL2 -0.10 0
C12 CTL5 -0.35 0
C13 CTL5 -0.35 0
C14 CTL5 -0.35 0
H11 HL 0.25 0
H12 HL 0.25 0
H21 HL 0.25 0
H22 HL 0.25 0
H23 HL 0.25 0
H31 HL 0.25 0
H32 HL 0.25 0
H33 HL 0.25 0
H41 HL 0.25 0
H42 HL 0.25 0
H43 HL 0.25 0
C15 CTL2 -0.08 1
H51 HAL2 0.09 1
H52 HAL2 0.09 1
P1 PL 1.50 2
O3 O2L -0.78 2
O4 O2L -0.78 2
O1 OSL -0.57 2
O2 OSL -0.57 2
C1 CTL2 -0.08 3
...
While in 4.5.4 this is
[ POPC ]
[ atoms ]
N NTL -0.60 0
C11 CTL2 -0.10 1
C12 CTL5 -0.35 2
C13 CTL5 -0.35 3
C14 CTL5 -0.35 4
H11 HL 0.25 5
H12 HL 0.25 6
H21 HL 0.25 7
H22 HL 0.25 8
H23 HL 0.25 9
H31 HL 0.25 10
H32 HL 0.25 11
H33 HL 0.25 12
H41 HL 0.25 13
H42 HL 0.25 14
H43 HL 0.25 15
C15 CTL2 -0.08 16
H51 HAL2 0.09 17
...
The charge groups do not have integer charge and are all one atom.
The beta version has groups that agree with the charmm groups and
have integer charge. Was this changed on purpose? The beta version
seems correct to me, but am I missing something as to why this change
would be made?
Thanks
--
Dr Thomas Piggot
University of Southampton, UK.
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