Dear Gromacs users
I want to calculate Potential Energy of segment of the structure.
For example, segment that coordinations in z axis are 7.2 Å in the structure.
I could specify that segment of atom numbers by writing index file.
But gmx energy has no option of specifying segments by index fil
Dear Bruce D. Ray
Thank you for replying to my question.
I understood that I should not include water molecules in submit file to
topolbuild
because water topology is given by spce.itp.
Then, should I give coordinates of water to *.gro file and delete parameters of
water in topology file
when
n water later,
> with the building blocks in e.g. the standard spce.itp.
>
> Chapter 5 of the GROMACS reference manual is the resource to look at what
> the various parameter quantities mean, but it is likely that you should not
> be attempting to supply water parameters.
&g
Dear gmx users,
I have questions about topology file parameters.
I tried get topology files with topolbuild. But I was required to fix the *.top
file
because H2O parameters were not given.
I could give some parameters in atoms and bonds, but I don't know some meanings
of parameters.
topology
Dear David van der Spoel
Thank you for giving me advice.
I'll choose TIP4P/Ice model and write its parameters on the topology files.
Sincerely.
Keisuke Ohki, senior student.
Dept. applied physics and physico-informatics., Keio University.
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Dear gromacs users
I have a question why topolbuild fails to read oxygen in H2O.
I want to make a topology file of methane hydrate structure with topolbuild and
run simulation in gromacs.
I used following command line:
./topolbuild -n ../HYDRATE_A -dir ../dat/gromacs -ff oplsaa -purge 0
.mol2
