[gmx-users] Effect of vdwradii.dat

Mark Abraham 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.


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