[gmx-users] Effect of vdwradii.dat
Mark.Abraham at anu.edu.au
Thu Jun 14 01:33:10 CEST 2012
On 14/06/2012 2:31 AM, Anna Duncan wrote:
> Hello all,
> I'm doing a membrane-protein simulation using MARTINI of the ADP/ATP
> carrier in a POPC/POPE membrane. After inserting the protein into the
> membrane I solvated the system using g_genbox. In order to prevent
> water beads from being placed within the bilayer, I made a local copy
> of vdwradii.dat with large vdw radii listed for acyl chain beads, as
> suggested in Justin Lemkul's useful membrane protein tutorial.
> However, I forgot to delete the local copy of vdwradii.dat before
> moving on to further stages (ie. energy minimisation, equilibration
> and the final run). Will this make a difference or is the information
> in vdwradii.dat only used for commands such as g_genbox and g_sas? Is
> there any way of checking this?
I expect there is no difference. You can prove this by re-making your
.tpr with a normal vdwradii.dat present and comparing both .tpr files
with gmxcheck. mdrun uses only things on its command line as inputs.
More information about the gromacs.org_gmx-users