[gmx-users] Fwd: About Justin Lipid-protein simulation tutorial
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 27 12:27:46 CEST 2012
On 6/27/12 1:23 AM, rama david wrote:
> Hi Gromacs Friends,
> I am doing Justin-lipid tutorialer
> In these the npt.mdp has a parameter
> refcoord_scaling = com
> Why these parameter is introduced in NPT of lipid-protein simulation
> and not use in Lysozyme in water simulation ???
It is used in the lysozyme tutorial. Some time ago, I was informed that the
line was missing from the .mdp file, so if you completed the tutorial during
that time, the line was missing. grompp should have produced an obvious
> Please give the detail on why to use these parameter??
If the reference coordinates are not scaled, you can get spurious contributions
to the virial and pressure. There is some discussion on this (admittedly not
much) in the manual.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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