[AMBER] weird asymmetries in solvent box

From: Thomas Charles Pochapsky <pochapsk.brandeis.edu>
Date: Sat, 15 Apr 2017 08:52:11 -0400

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


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Received on Sat Apr 15 2017 - 06:00:03 PDT
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