[AMBER] lj1264 pmemd.cuda

From: Andreas Tosstorff <andreas.tosstorff.cup.uni-muenchen.de>
Date: Tue, 31 Jan 2017 10:40:32 +0100

Hi all,

I want to run some REMD simulations with a peptide/Zinc system.

I wanted to use th 12-6-4 LJ-Type Nonbonded model.

I generated the parm7 and crd files according to the manual and ran my
first simulation using pmemd.cuda.

lj1264 is set to 1 and the simulation ran without any errors, however it
did not produce the expected outcome, meaning that Zn2+ would bind to a
HIE residue in its proximity.

I read in the manual that lj1264 is not supported by pmemd.cuda.

Is this information outdated or is pmemd.cuda just ignoring lj1264=1?

Should I rather use 12-6 LJ-Type with pmemd.cuda?

Kind regards,


M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Tel.: +49 89 2180 77059
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Received on Tue Jan 31 2017 - 02:00:03 PST
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