varsha gautham wrote:
Dear gmx-users,
Am doing a simulation of DPPC bilayer with a polymer. I read from
various papers that SPC is the best water model for lipids and GROMOS
87 is the best force field adapted for the lipids. So i made
use of SPC and gromos 87 in my simulation .But am not clear with
GROMOS 87 file format and about SPC.
Gromos87 (via ffgmx) is deprecated and should not be used for new simulations.
You should at the very least be using the Berger lipid parameters, which are a
modification of Gromos87. Even these are a bit old, and a Gromos96
parameterization for lipids has recently appeared in JCTC.
Recently for one of the users, they have provided links to know about
water model and force fields.But am not getting a clear idea from any
of these links.Please if anyone can give me a
link or description of GROMOS 87 file format and SPC water model,I
will be very thankful.
Discussions of file formats can be found in the Gromacs manual, and by visual
inspection of the contents of the file. Sections and columns within those
sections are labeled quite clearly.
My question is ,
1. How gromos 87 file format differ from others?Are there any free
reviews available online?
It is not the file format that differs, it is the contents of the file and how
the parameters were derived.
If so please provide me those links.
2 .How is SPC model differs from TIP3p and TIP4p?
Google is your friend. Try searching for "water models," and I think you will
find what you are looking for.
-Justin
-varsha
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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