[gmx-users] tip3p itp file parameters

Sai Pooja 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
files.
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?
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-October/055332.html
>
>
> 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.
>
> -Justin
>
>
> Pooja
>>
>>
>> --
>> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101104/2e912dd1/attachment.html>


More information about the gromacs.org_gmx-users mailing list