sarbani chattopadhyay wrote:
Hi everybody,
My question is regarding the consequence of a
mistake of mine.
I wanted to run gromacs with "charmm" force field and "tip3p" water model.
I had posted a query as to how can I get the "tip3p.gro" file. I was
suggested to equlibrate
the "spc216.gro" file for 1ns.
However, what I did was that I equilibrated the "spc216.gro" file but
while giving the
"pdb2gmx" command , I gave the option "-water spc". I know this was
extremely stupid on
my part.
Thus now the water model selected is spc ie. it refers to "spc.itp" but
uses the equlibrated
file "spc216.gro"
Will this affect my simulation adversely? Please suggest as what can be
the probable
consequences.
Force fields are designed for use with specific water models. Using CHARMM +
SPC is not a valid combination (see below).
Moreover while going through some of the tutorials such as " Molecular
Dynamics
Simulations" by Erik R. Lindahl, I found that "spc216.gro" can be used
for "tip3p"water
model, if we correctly select "tip3p" as the water model.
True.
I think if I choose "tip3p" as the water model and the equlibrated
"spc216.gro" file , then I
should get thecorrect results.Is this so?
Almost. There is something unique about the CHARMM water molecule - there are
L-J parameters for the hydrogens. Therefore, the water model you need is
tip3p-charmm.itp (packaged with the CHARMM for GROMACS download that you
probably got from the downloads site). So you will need to manually edit your
.top file, regardless of what pdb2gmx gives you, to include this proper water model.
-Justin
Thanks in advance.
Sarbani
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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