[gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 27 13:19:50 CEST 2012

On 6/27/12 7:16 AM, rama david wrote:
> Thank you Justin,
> But you not added these parameter to the
> Umbrella sampling NPT file.
> Is any reason not to use these parameter  in Umbrella sampling??

If it is missing, it's a simple typographical omission.  I have adapted these 
tutorials over many years and occasionally something like this slips through the 
cracks.  Hence why it's always important to pay attention to the warnings grompp 
prints out.

> I run the simulation of peptide withought any
> refcoord_scaling = com in mdp  file
> and now  is it will affect result  significantly??
> Is it wrong simulation???
> How to check these parameter affect my result sensitivity???

The pressure might be slightly off.



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


More information about the gromacs.org_gmx-users mailing list