[gmx-users] error with cut-off length using verlet scheme in stochastic dynamics simulation

[Amanda Parker]

Thank you for your reply! I did not realize that rcoulomb and rvdw were
relevant and will look into them. Below is the full text of my mdp file:



; RUN CONTROL PARAMETERS
integrator               = sd  ; Stochastic Langevin dynamics
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.02
nsteps                   = 1000000 ;
; For exact run continuation or redoing part of a run
init_step                = 0
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part          = 1
; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 100
; group(s) for center of mass motion removal
comm-grps                = system

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd_fric                  = 0
ld_seed                  = 1735
; Groups to couple separately
tc_grps                  = system
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.02
ref_t                    = 300

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
; Output frequency for energies to log file and energy file
nstlog                   = 10000
nstcalcenergy            = 10000
nstenergy                = 10000
; Output frequency and precision for .xtc file
nstxtcout                = 10000
xtc-precision            = 1000
; This selects the subset of atoms for the .xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps                 =
; Selection of energy groups
energygrps               =


nstlist     = 10
ns_type     = grid
rlist       = 2.0
rcoulomb    = 2.0
rvdw        = 2.0

; PME electrostatics parameters
cutoff-scheme = Verlet
coulombtype     = Cut-off
pbc                      = xyz

On Wed, Sep 28, 2016 at 12:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/28/16 3:12 PM, Amanda Parker wrote:
>
>> Hello,
>>
>> I am trying to run a stochastic dynamics simulation and am getting the
>> error:
>>
>> "The cut-off length is longer than half the shortest box vector or
>>   longer than the smallest box diagonal element. Increase the box size or
>>   decrease rlist."
>>
>> I've increased my box vectors to 100 nm, 100 nm, 100 nm (as I see
>> confirmed
>> at the bottom of my .gro file). I am using the Verlet cut-off scheme,
>> which
>> as I understand it makes rlist irrelevant and uses its own default cut-off
>> length (perhaps of 0.005?), unless I specify verlet-buffer-tolerance = -1.
>> I have tried using no verlet-buffer-tolerance line, as well as using
>> verlet-buffer-tolerance = -1 and setting rlist = 2. Both of these options
>> continue to give the error above.
>>
>> How do I check the cut-off length for Verlet scheme? Without being able to
>> do that, I cannot confirm that the cut-off length is indeed longer than
>> half the shortest box vector. That said, I would be surprised if the
>> cut-off length was longer than 50 nm.
>>
>> I'm happy to include copies of any files that you feel are necessary to
>> understanding this problem. At this point it seems the only information
>> necessary are the box vectors and cut-off length (and in this case the
>> fact
>> that I'm using Verlet), but I may be wrong.
>>
>> Any insight is much appreciated.
>>
>>
> Post the full text of your .mdp file.  rlist isn't the only cutoff that
> matters. rcoulomb and rvdw can trigger the problem, too.  There's clearly
> something weird going on.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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