[gmx-users] truncating LJ potentials

[Irem Altan]

Hi,

I decided to test this for a system of sodium and chloride ions (based on http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf ):

Guyana Rwanda Oman Macau Angola Cameroon Senegal
    8
    1NA      Na    1   0.131   0.116   0.051
    2NA      Na    2   0.137   0.111   0.047
    3NA      Na    3   0.124   0.110   0.053
    4NA      Na    4   0.131   0.115   0.051
    5CL      Cl    5   0.009   0.109   0.051
    6CL      Cl    6   0.000   0.111   0.049
    7CL      Cl    7   0.010   0.112   0.061
    8CL      Cl    8   0.009   0.109   0.052
   0.50000   0.50000   0.50000

I’m trying to do a test energy minimization but grompp gives me the following errors:

ERROR 1 [file minim.mdp]:
  With Verlet lists only cut-off and PME LJ interactions are supported


ERROR 2 [file minim.mdp]:
  With Verlet lists only cut-off, reaction-field, PME and Ewald
  electrostatics are supported


NOTE 1 [file minim.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 2498183954

-------------------------------------------------------
Program gmx grompp, VERSION 5.1.2
Source code file: /Users/irem/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/topio.c, line: 755

Fatal error:
Syntax error - File topol.top, line 21
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Does this mean I can’t use Verlet neighbor lists with custom non-bonded interaction potentials? And does that in turn mean that I can’t use GPUs in my simulations?

Also, could you help me figure out how to fix the error in the topology file? The contents of the relevant files are as listed below.

Best,
Irem

———————————————————————————

minim.mdp:
—————————

; minim.mdp - used as input into grompp to generate em.tpr
integrator      = steep         ; Algorithm (steep = steepest descent minimization)
emtol           = 1000.0        ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep      = 0.01      ; Energy step size
nsteps          = 50000         ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist             = 1             ; Frequency to update the neighbor list and long range forces
cutoff-scheme   = Verlet
ns_type             = grid              ; Method to determine neighbor list (simple, grid)
rcoulomb            = 1.0               ; Short-range electrostatic cut-off
rvdw                = 1.0               ; Short-range Van der Waals cut-off
pbc                     = xyz           ; Periodic Boundary Conditions (yes/no)

; custom potentials
vdw-type = user
coulombtype = user
energygrps = sodium chloride
energygrp_table = sodium sodium chloride chloride

topol.top:
-----------------

[ atomtypes ]
Na      Na   22.99    1   A  1.0e-03  1.0e-06
Cl      Cl   35.45   -1   A  2.0e-03  9.0e-06

[ nonbond_params ]
Na      Cl   1   2.22213706E-03  3.43076954E-06

[ moleculetype ]
; Name            nrexcl
Ion_chain_A         3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
; residue   1 NA  rtp NA   q +1.0
     1         Na      1     NA     Na      1          1      22.99   ; qtot 1
; residue   2 NA  rtp NA   q +1.0
     2         Na      2     NA     Na      2          1      22.99   ; qtot 2
; residue   3 NA  rtp NA   q +1.0
     3         Na      3     NA     Na      3          1      22.99   ; qtot 3
; residue   4 NA  rtp NA   q +1.0
     4         Na      4     NA     Na      4          1      22.99   ; qtot 4
; residue   5 CL  rtp CL   q -1.0
     5         Cl      5     CL     Cl      5         -1      35.45   ; qtot 3

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

[ system ]
; Name
Protein

[ molecules ]
; Compound        #mols
Ion_chain_A         1

index.ndx:
-----------------

[ sodium ]
1 2 3 4
[ chloride ]
5 6 7 8