I am running a constant pressure equilibration of a solvated protein in
Sander, the run truncated with the following message:
/In this slab, Atoms found: 6578 Allocated: 5629//
//
//***** Processor 18//
//***** System must be very inhomogeneous.//
//***** Readjusting recip sizes.//
// In this slab, Atoms found: 6345 Allocated: 5629//
//
//***** System must be very inhomogeneous.//
//***** Readjusting recip sizes.//
// In this slab, Atoms found: 6733 Allocated: 5629//
//
//***** Processor 16//
//***** System must be very inhomogeneous.//
//***** Readjusting recip sizes.//
// In this slab, Atoms found: 5630 Allocated: 5629/
Looking at the rst7 coordinates, the solvent has developed strange
concavities, with some of the solvent edges very close to the surface of
the protein.
Here is the input file:
1ns equilibium with constant pressure
&cntrl
imin=0,
irest=1,
nstlim=500000,
dt=0.002,
ntc=2,
ntx=5,
ntf=2,
nmropt=0,
ntpr=100,
ntwx=2000,
cut=16,
ntb=2,
ntp=1,
tautp=2.0,
igb=0,
ntt=3,
gamma_ln=2.0,
tempi=300.0,
temp0=300.0,
/
&wt type='END' /
LISTOUT=POUT
&end
Any suggestions?
Thanks,
Tom Pochapsky
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 15 2017 - 06:00:03 PDT
