sarbani_c84 at rediffmail.com
Wed Aug 13 09:39:26 CEST 2008
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
Thus now the water model selected is spc ie. it refers to "spc.itp" but uses the equlibrated
Will this affect my simulation adversely? Please suggest as what can be the probable
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.
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?
Thanks in advance.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users