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On 21/07/2011 4:26 PM, E. Nihal Korkmaz wrote:
<blockquote
cite="mid:CAK7hcucixyH-LjTSCv8A=2dK5EXv_DTD2sozAPLa2OJxwu-Fdg@mail.gmail.com"
type="cite">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.<br>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAK7hcucixyH-LjTSCv8A=2dK5EXv_DTD2sozAPLa2OJxwu-Fdg@mail.gmail.com"
type="cite">
<br>
Thanks,<br>
Nihal<br>
<br>
<div class="gmail_quote">On Wed, Jul 20, 2011 at 11:05 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im">On 21/07/2011 12:59 PM, E. Nihal Korkmaz
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear all,<br>
<br>
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)<br>
</blockquote>
<br>
</div>
Why not check out the primary literature? Search GROMACS
manual for SPC, follow the reference link for the relevant
citation.<br>
<br>
Mark<br>
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</div>
<br>
<br clear="all">
<br>
-- <br>
Elif Nihal Korkmaz<br>
<br>
Research Assistant <br>
University of Wisconsin - Biophysics <br>
Member of Qiang Cui & Thomas Record Labs<br>
1101 University Ave, Rm. 8359<br>
Madison, WI 53706<br>
Phone: 608-265-3644<br>
Email: <a moz-do-not-send="true" href="mailto:korkmaz@wisc.edu"
target="_blank">korkmaz@wisc.edu</a><br>
<br>
<br>
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