chris.neale at mail.utoronto.ca
Wed Jul 11 03:37:35 CEST 2012
I always use refcoord_scaling = com because of the warning that refcoord_scaling = no gives problems:
quoting http://manual.gromacs.org/online/mdp_opt.html#pc :
"Note that with this option the virial and pressure will depend on the absolute
positions of the reference coordinates."
I don't see why anyone would want to use refcoord_scaling = all , which it seems to me would deform
your protein. I actually think that any use of refcoord_scaling = all should throw a warning so that the
user would have to acknowledge this via -maxwarn to ensure that they didn't get unexpected behaviour.
-- original message --
On 7/10/12 5:48 PM, Katie Maerzke wrote:
> Hi all -
> I'm new to Gromacs (and MD). I can't figure out whether or not
> refcoord_scaling is important for an NpT simulation. In an MC simulation,
> when the volume changes, the coordinates of the molecules are also scaled.
> Does refcoord_scaling control how to handle scaling the molecular coordinates
> (e.g., scale all coordinates or scale based on COM), or does it do something
> else? Is it even important? I've searched the manual and the user forum,
> but I haven't found an answer to my question.
The important distinction is between reference coordinates and the actual
coordinates of the atoms. When employing position restraints, the restraint
potential is based on the reference positions of the atoms. It is these that
are updated based on the refcoord_scaling option. In most cases, the box
shouldn't change drastically, and if it does, you have bigger problems. Thus, I
imagine the contribution to energy is likely small, but I have never tested this
myself. In theory, if the reference coordinates are not updated correctly, you
will get incorrect contributions to the virial and thus some errors in pressure
This is my understanding of the implementation; if it is incorrect or
incomplete, hopefully someone will chime in.
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