I've solvated and neutralised my protein and water system and I'm using PME for my electrostatics. I'm trying to use Block to turn off some VDW interactions, in conjunction with some adiabatic mapping. I'm leaving out the adiabatic mapping here for parsimony.
My input and output files are attached. I'm using C41a2 on a Mac OSX Yosemite.
Problem: Whenever I try and minimize my system the coordinates do not change but the total energy (in particular the EWKSum) blows up (to 'infinity' eventually). When I turn off Block, everything works fine.
With Block I'm defining a region of 3 atoms in which the VdW interactions are set to zero. The scaling between this block and the 'outer' block is set to 1. The total charge on the group is -1. The overall charge on the system is 0.0
Things I've tried but the energy still blows up:
1. Initializing BLOCK before and after my crystal/image setup.
2. Keeping the BLOCK setup the same except changing the scaling from 0 to 1 for the VdW interactions with the region.
3. Increased the Cutoff from 30 to 40 to 60 in my crystal build command.
4. Used ABNR instead of SD.
I've read the latest docs on Block which say that the 'image' command should work with Block but the 'Crystal' command might not. I don't particularly understand this as I thought the two went hand in hand.
Any help would be greatly appreciated.
EDIT - I just noticed 'fswitch' was specified for the electrostatic interactions. Taking that out didn't change anything however.
EDIT - looked again at the previous thread on this, here
I misread the date and assumed it was 10 years ago and had been fixed by now. The latest docs do say it should work however.
EDIT - just tried using the slower Standard Ewald summation for the non-bonded interactions. I haven't fully tested it but it appears to work.
set kppa 0.34
calc kmx int( @kppa*@xdim ) !XDIM = x-dim for crystal.
calc kmy int( @kppa*@ydim )
calc kmz int( @kppa*@zdim )
NBONDED inbfrq -1 imgfrq -1 nbxmod 5 - ! C36 DEFAULTS
atom cdiel - !fshift - ! use atom based electrostatics, C36 DEFAULTS
vatom vdistance vfswitch - ! C36 DEFAULTS
elec ewald kappa @kppa spline nopm kmxx @kmx kmxy @kmy kmxz @kmz - ! standard Ewald SUMMATION
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 - ! C36 DEFAULTS
cutim 14.0 - ! must be same as cutnb
eps 1.0 e14fac 1.0 wmin 1.5 ! C36 DEFAULTS