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.
Mark
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