[gmx-users] reaction field: lots of warnings and errors

[w.j.schravendijk at students.pharm.uu.nl]

Dear Gromacs users,

For my 26-residue peptide with +6 charge in a box with 9000 water
molecules, I get the following warnings using a reaction field and
flex_spc water:

Warning: 1-4 interaction at distance larger than 1

Step 2  Warning: pressure scaling more than 1%, mu: 1.46747e+14
1.46747e+14 1.46747e+14

(the next one shows up several times:)

Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.

(And then:)

Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 214]

Lots of things going wrong here... Runs using a simple cut-off won't give
these kind of problems, but are less accurate. I guess I'll have to stay
using the cut-off method for this?

Groetjes, Pim

Below is a part of my .mdp file. I've tried to adjust things in various
ways, (really short timestep!), but it didn't seem to help...

; -- PREPROCESSING --
title                    =
cpp                      = /lib/cpp
include                  = -I../top
define                   = -DFLEX_SPC
;
; -- RUN CONTROL --
;
integrator               = md
dt                       = 0.0002
nsteps                   = 50000
;

;
; -- NEIGHBOUR SEARCHING --
;
nstlist                  = 10
ns_type                  = grid
rlist                    = 0.7 ; lager dan rvdw
;
; -- ELECTROSTATICS / VDW --
;
coulombtype              = Generalized-Reaction-Field
rcoulomb                 = 0.8
rvdw                     = 1.4
epsilon_r                = 54 ; as in article Walser 2001
;
; -- COUPLING --
;
tcoupl                   = Berendsen
tc-grps                  = Protein      SOL
tau_t                    = 0.1  0.1
ref_t                    = 300  300
Pcoupl                   = Berendsen
tau_p                    = 10.0
compressibility          = 4.5e-5
ref_p                    = 1.0