[gmx-users] truncating LJ potentials

[Mark Abraham]

Hi,

On Thu, Jul 14, 2016 at 11:37 PM Irem Altan <irem.altan at duke.edu> wrote:

> 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?


Correct (as I said in my first sentence in this thread).


> And does that in turn mean that I can’t use GPUs in my simulations?
>

Correct. We have been working on this, but it isn't ready yet.


> 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.
>

The error is on point - you haven't honored the required order for
directives (see examples and text in chapter 5), e.g. because [ defaults ]
must be first.

Mark

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
>
>
> --
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