Jayeeta Ghosh wrote:
Dear Gromacs Users,
I am having similar problem that was reported by Sarah about a year ago.
I am using Gromacs4.0.7. I am using the following command to make the
index file.
It would be more efficient if you posted a link to the report of the issue. If
it is the problem I am thinking of, the output was not generated because of an
incorrect index file, which may or may not be the case here.
make_ndx -f dppc128.gro -o sn1.ndx
> a C34
> a C36
> ...
> a C50
> del 0-2
> q
I am using following command to calculate the order parameter.
g_order -n sn1.ndx -od
I am using all other default input file names. I am only getting two
output files: sg-ang.xvg and sk-dist.xvg, no order.xvg.
I am not sure how to get around this.
That's very weird, the files you're getting are the optional output, which you
haven't specified. If you add -o and -od (for both order.xvg and deuter.xvg),
is the result any different? Does your system indeed contain only lipids?
-Justin
I would really appreciate any help.
Thanks,
Jayeeta
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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