[gmx-users] lipid-SPC/SPCE interactions in lipid.itp (Tieleman website)

[Justin Lemkul]

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

-- 
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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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