On 3/5/13 7:48 PM, fciocco wrote:
Hi,
I have a quick question:
the ;; lipid-SPC/SPCE interactions section :
LO OW 1 2.50200e-03 2.06700e-06
LOM OW 1 2.50200e-03 2.06700e-06
LNL OW 1 2.98000e-03 3.25900e-06
LC OW 1 3.59800e-03 6.04400e-06
LH1 OW 1 3.26800e-03 5.71200e-06
LH2 OW 1 4.30700e-03 8.17000e-06
LP OW 1 4.92600e-03 8.21000e-06
LOS OW 1 2.60500e-03 2.24100e-06
LP2 OW 1 3.94400e-03 7.80300e-06
LP3 OW 1 4.82100e-03 9.53900e-06
LC3 OW 1 4.97800e-03 9.85000e-06
LC2 OW 1 3.96900e-03 6.93800e-06
in the [ nonbond_params ] section in lipid.itp file downloaded from
Tieleman's site should be include in the ffnonbonded.itp file?
the KALP-DPPC tutorial says: In the [ nonbond_params ] section, you will
find the line ";; parameters for lipid-GROMOS interactions." Delete this
line and all of the subsequent lines in this section; but I'm not 100% sure
if I have to delete the lipid-SPC/SPCE interactions lines.
The C6/C12 parameters for the OW atom type are slightly different in 53A6 than
they were in Gromos87 (looks like mostly rounding differences in the nonbonded
parameter files). The parameters listed in lipid.itp are based on Gromos87, so
if you're using 53A6, then do as the tutorial says and delete the lines. The
necessary interactions will simply be calculated according to normal combination
rules.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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