Hi
I have decided to make a data file for a simulation box of water-methanol mixture. I will appreciate to help me to find best and easiest way to write the data file.I mean,which package is appropriate (topotools, packmol,moltemplate etc…)?
Thank you,
Mohammadreza
Hi
I have decided to make a data file for a simulation box of water-methanol
mixture. I will appreciate to help me to find best and easiest way to write
the data file.I mean,which package is appropriate (topotools,
packmol,moltemplate etc..)?
probably either. just keep in mind, that there are no shortcuts here.
the important step is not so much how you generate the initial
configuration, but how you equilibrate the resulting system to reach
the proper density and a suitable equilibrium structure that is
consistent for the state, viscosity and the force field you are using.
if you worry about computational efficiency, start from a small
system. equilibrate it. then replicate it and re-equilibrate. rinse
and repeat, until you have the desired size. starting from the target
size directly is guaranteed to require significantly more CPU time.
that is just a common sense consideration.
axel.
Thanks Axel.
Well said.
I suppose the only other issue to consider is the force field. Different molecule builders support different force-fields. At the moment, if im not mistaken, topotools can generate force-fields pareters for the CHARMM force field, and moltemplate can generate OPLSA and AMBER/GAFF parameters. But these lists will change over time, and you can add support for new force fields. Other molecule builders are are on the LAMMPS pre/post web link. (There’s also Molecular Dynamics Studio.)
But for such a simple system, you can probably assign all of the force-fields parameters manually, so it really does not matter.
If you have trouble with these programs post a question here and it will usually get answered by one of us.
Good luck
andrew
Thanks Axel.
Well said.
I suppose the only other issue to consider is the force field. Different
molecule builders support different force-fields. At the moment, if im not
mistaken, topotools can generate force-fields pareters for the CHARMM force
no. topotools directly does not generate or assign *any* kind of
parameters. that is a deliberate choice, as those often need to follow
different conventions for different MD codes. for CHARMM this actually
isn't needed, the parameters are assigned at run time from a parameter
file, so all that is required to do is to assign atom type labels (and
those have to match what is given in the CHARMM parameter file). there
is the special case of the writegmxtop function that can write charmm
force field topologiy files for gromacs, but that is a singular
exception (at the moment).
field, and moltemplate can generate OPLSA and AMBER/GAFF parameters. But
these lists will change over time, and you can add support for new force
fields. Other molecule builders are are on the LAMMPS pre/post web link.
(There's also Molecular Dynamics Studio.)
please note that for many water-alcohol mixtures there are custom
parameter sets specifically tuned for those cases that will improve on
what generic force fields can offer.
axel.
Thanks Axel.
Well said.
I suppose the only other issue to consider is the force field. Different
molecule builders support different force-fields. At the moment, if im not
mistaken, topotools can generate force-fields pareters for the CHARMM forceno. topotools directly does not generate or assign *any* kind of
parameters. that is a deliberate choice, as those often need to follow
different conventions for different MD codes.
Oops, sorry. Okay I see that it generates gromacs files.
for CHARMM this actually
isn't needed, the parameters are assigned at run time from a parameter
file, so all that is required to do is to assign atom type labels (and
those have to match what is given in the CHARMM parameter file).
Somebody may eventually ask for more clarification (or a tutorial) on
this topic.
there
is the special case of the writegmxtop function that can write charmm
force field topologiy files for gromacs, but that is a singular
exception (at the moment).
Cool.
Thanks for the clarification. I know that whenever a new force-field
gets added to moltemplate, I always spam the mailing list about it.
So please keep us updated about topotools.
-Andrew