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

[Facundo Ciocco Aloia]

thanks Justin,

best regards,

2013/3/5 Justin Lemkul <jalemkul at vt.edu>

>
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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