[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
> http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
> 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 
warning, however.

> 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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