[gmx-users] Error in NVT equilibration

Tue Sep 18 11:42:06 CEST 2018

Hi,

As I am using the GROMOS froce field, I constrained all bonds as suggested. However, I obtained the same error.

I copy the .mdp file in case there are errors and you can help me to find them:

title                   = Lipid NVT equilibration
define                  = -DPOSRES  ; position restrain the Lipid
; Run parameters
integrator              = md        ; leap-frog integrator
nsteps                  = 6667      ; 2 * 50000 = 100 ps
dt                      = 0.015     ; 2 fs
; Output control
nstxout                 = 500       ; save coordinates every 1.0 ps
nstvout                 = 500       ; save velocities every 1.0 ps
nstenergy               = 500       ; save energies every 1.0 ps
nstlog                  = 500       ; update log file every 1.0 ps
; Bond parameters
continuation            = no        ; first dynamics run
constraint_algorithm    = lincs     ; holonomic constraints
constraints             = all-bonds   ; bonds involving H are constrained
;shake_tol              = 0.0001
lincs_iter            = 1            ; accuracy of LINCS
lincs_order            = 4            ; also related to accuracy
; Nonbonded settings
cutoff-scheme           = Verlet    ; Buffered neighbor searching
ns_type                 = grid      ; search neighboring grid cells
nstlist                 = 10        ; 20 fs, largely irrelevant with Verlet
rlist                   = 1.4
rcoulomb                = 1.2       ; short-range electrostatic cutoff (in nm)
rvdw                    = 1.2       ; short-range van der Waals cutoff (in nm)
DispCorr                = EnerPres  ; account for cut-off vdW scheme
vdwtype                 = Cut-off
vdw_modifier            = Force-switch
rvdw_switch             = 1
; Electrostatics
coulombtype             = PME       ; Particle Mesh Ewald for long-range electrostatics
ewald-rtol              = 1e-6
pme_order               = 4         ; cubic interpolation
fourierspacing          = 0.16      ; grid spacing for FFT
; Temperature coupling is on
tcoupl                  = V-rescale             ; modified Berendsen thermostat
tc-grps                 = System   ; two coupling groups - more accurate
tau_t                   = 0.1               ; time constant, in ps
ref_t                   = 298               ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl                  = no        ; no pressure coupling in NVT
; Periodic boundary conditions
pbc                     = xyz       ; 3-D PBC
; Velocity generation
gen_vel                 = yes       ; assign velocities from Maxwell distribution
gen_temp                = 298       ; temperature for Maxwell distribution
gen_seed                = -1        ; generate a random seed
;Simulated annealing
annealing               = single
annealing_npoints       = 2
annealing_time          = 0 1
annealing_temp         = 278 298

Thank you in advance,

C.

________________________________
De: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> en nombre de Justin Lemkul <jalemkul at vt.edu>
Enviado: lunes, 17 de septiembre de 2018 14:06:24
Para: gmx-users at gromacs.org
Asunto: Re: [gmx-users] Error in NVT equilibration

On 9/17/18 8:04 AM, Vytautas Rakeviius wrote:
>   I think your attachment to email was lost during re-transfer and it would be nice to see that, but I think what you need is:constraints                 = all-bondsIn that mdp file.

That depends on the force field convention. It is not universally
appropriate to constrain all bonds (and certainly should not be the
"solution" to just "make the warning go away"), and the warning from
grompp may not actually be the source of any problem.

-Justin

>      On Friday, September 14, 2018, 4:07:43 PM GMT+3, Gonzalez Fernandez, Cristina <cristina.gonzalezfdez at unican.es> wrote:
>
>   Dear Gromacs users,
>
>
> I am trying to perform a nvt equilibration, but when I generate the .tpr file I get a warning indicating that a bond is oscillating too fast:
>
>
> The bond in molecule-type MOL_1 between atoms 38 C21 and 39 O22 has an estimated oscillational period of 2.4e-02 ps, which is less than 5 times the time step of 1.5e-02. Maybe you forgot to change the constraints mdp option.
>
>
>
> I have ignored it with the -maxwarn option and I obtain the .tpr file. However, when I run the simulation I obtain this error?
>
>
> Too many LINCS warnings (1630)
>
>
>
> Are the error and the warning related? How could I solve the Lincs error and the warning?
>
>
> I attach the .mdp file.
>
>
>
>
> Thank you in advance,
>
>
> C.

--
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
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