On 21/07/2011 4:26 PM, E. Nihal Korkmaz wrote:
Thanks but I already checked the literature. What I want to do is, to
be able to trace down the parameters in the nonbonded file like it can
be done for any version of gromos. There are slight changes among
different force fields and I'd like to be able to find that. When I
find where it reads spc/e parameters for c27, i want to play with the
parameters that's why i am asking the file read.
Anything that's not found in spce.itp is looked up from ffbonded.itp or
ffnonbonded.itp. I can't think of a single case where the charges in
ffnonbonded.itp are used, so there's probably no reason to expect them
to be correct. You should satisfy yourself that GROMACS is implementing
the correct form of SPC/E found in the primary literature. However,
since CHARMM was not parameterized with SPC/E, there probably is no
particular correct form to use.
Mark
Thanks,
Nihal
On Wed, Jul 20, 2011 at 11:05 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:
On 21/07/2011 12:59 PM, E. Nihal Korkmaz wrote:
Dear all,
I was trying to see the LJ parameters for SPC/E water in
Charmm27.ff implementation in Gromacs. In the ffnonbonded.itp
file i can see parameters for TIP3P, TIP4P, SPC but not for
SPC/E. Does SPC/E use the same parameters with SPC? (but the
charges listed in the ffnonbonded.itp is different than the
ones listed in spce.itp)
Why not check out the primary literature? Search GROMACS manual
for SPC, follow the reference link for the relevant citation.
Mark
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Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
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