AMBER Archive (2007)

Subject: RE: AMBER: Implicit/Explicit solvation

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Nov 21 2007 - 10:10:58 CST

Hi Eddie,

I haven't tried running such simulations but I'll try and offer some
suggestions.

> Sample water CAP simulation with PB reaction field correction
> &cntrl
> ntx=1, irest=0, imin=0,
> ntpr=500, ntwx=500, ntwr=5000,
> nstlim=100, dt=0.001,
> ntt=1, temp0=10, tempi=10, tautp=0.1,
> igb=10, ntb=0, cut=0, fcap=1.0, ivcap=0,

cut=0? Is this really what you want? Maybe it is overridden by the cutres
and cutnb values in the &pb namelist but you should probably check this just
to make sure.

> PB warning in pb_miccg(): CG maxitn exceeded!
>
>
> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 1 NaN NaN 0.0000E+00 N
> 1
>
> BOND = 515.0425 ANGLE = 1263.6023 DIHED =
> 4672.6459
> VDWAALS = ************* EEL = -35804.5153 EPB
> = NaN
> 1-4 VDW = 2355.3258 1-4 EEL = 24060.2189 RESTRAINT
> =
> 0.0000
> ECAVITY = 0.0000 EDISPER = 0.0000
>
>
> Any idea what is causing this?.

My first guess is that your initial structure is bad such that you have two
atoms overlapping. Hence why the VDWAALS terms is so large (*'s mean too
large to be printed). Does this calculation work as a simple gas phase
solvent cap run? Without the PB? You should try this first and then take a
look at your starting structure to see if you can see a problem with it. I
would particularly focus on the area around atom 1 since this is printed as
having the highest force in the output above.

All the best
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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