[gmx-users] Effect of vdwradii.dat

Anna Duncan anna.duncan at mrc-mbu.cam.ac.uk
Wed Jun 13 18:31:04 CEST 2012

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?



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