[gmx-users] tip3p itp file parameters
saipooja at gmail.com
Thu Nov 4 20:36:39 CET 2010
Thanks Justin. I was just making sure that I was modifying the relevant
On Thu, Nov 4, 2010 at 2:17 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Sai Pooja wrote:
>> When using the charmm forcefield, the following is the case:
>> 1. ffnonbonded.itp - has listed paramters for tip3p (and other water
>> models) OWT3 and HWT3
>> 2. ffbonded.itp - does not have paramters for OWT3 and HWT3
>> Does this mean:
>> 1. nonbonded parameters for tip3p are read from ffnonbonded.itp for ALL
>> nonbonded interactions OR
>> for water-water interactions are read from tip3p.itp file and for
>> protein-water are read from ffnonbonded.itp?
> Nonbonded interactions are applied uniformly, unless they are modified in a
> specific [nonbond_params] directive. Isn't this something we've worked
> through before?
> 2.bonded paramters for tip3p are read from tip3p.itp file?
> Bonded parameters for water models are really only relevant if using a
> flexible model (which you shouldn't). Otherwise, the SETTLE algorithm
> simply fixes the geometry. This is all determined by the #ifdef FLEXIBLE
> statement in, for instance, tip3p.itp.
>> Quaerendo Invenietis-Seek and you shall discover.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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Quaerendo Invenietis-Seek and you shall discover.
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