[gmx-users] tip3p

Justin Lemkul jalemkul at vt.edu
Sun Mar 9 23:25:43 CET 2014

On 3/9/14, 5:54 PM, Chetan Mahajan wrote:
> Hi Mark,
> Thanks for the reply. Now, 1983 article by Jorgensen gives parameters for
> rigid tip3p, whereas I am seeking that for flexible tip3p. Force constant
> is not mentioned in 1983 article by Jorgensen. The article that I cited in
> #1 point below gives these parameters for modified tip3p. I do not
> understand why these are different from those in tip3p files in gromacs
> installed. Is there any other article describing flexible tip3p parameters?

This is a question that has been asked several times on the list.  The simple 
answer is: there appears to be no known citation for the flexible TIP3P 
parameters in Gromacs.  The development log indicates they were added in 2003, 
but no reference was supplied in the commit message.  Early force fields were 
often passed around personally between developers, with few details published, 
so some force fields are (unfortunately) poorly documented.  Nowadays, in the 
time of Supporting Information, explicit parameters are usually published in full.

The Jorgensen model is indeed rigid, and subsequent studies have introduced 
flexibility.  There are several parameter sets available based on different 
groups' models.  If you're interested in flexible TIP3P for whatever reason, 
it's best to implement those parameters correctly.


>>> 3. That used by acpype tool while converting amber input files to gromacs
>>> input files.( 462750.4 kJ/(mol.nm2))

This is the force constant for generic alcohol (OH-HO) bond stretching in AMBER. 
  As I mentioned before, referring to the actual force field files (ffbonded.itp 
in this case) provides you with this information.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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