On 4/23/20 3:01 PM, lazaro monteserin wrote:
I am trying to run a temperature equilibration of my system and I get the
following error:

=======================
NOTE 1 [file nvt.mdp]:
   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
   nstcomm to nstcalcenergy

NOTE 2 [file nvt.mdp]:
   Center of mass removal not necessary for Andersen.  All velocities of
   coupled groups are rerandomized periodically, so flying ice cube errors
   will not occur.

ERROR 1 [file nvt.mdp]:
   nstcomm must be 1, not 100 for Andersen, as velocities of atoms in
   coupled groups are randomized every time step
=======================
  but I don't even have in my nvt.mdp any values for the nstcomm or
restriction of center of masses translations or rotation. So I honestly do
not know what is happening here.

Do anybody have an idea of what is going on?

For any settings no explicitly listed, the defaults are used. See the manual:

http://manual.gromacs.org/current/user-guide/mdp-options.html

-Justin

This are the parameters for my cvt.mdp:

======================================================
define                  = -DPOSRES  ; position restrain for waters
; Run parameters
integrator              = md-vv     ; velocity Verlet algorithm
nsteps                  = 50000     ; 2 * 50000 = 100 ps
dt                      = 0.002     ; 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             = h-bonds   ; bonds involving H are constrained
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        ; 1 fs, largely irrelevant with Verlet
rcoulomb                = 333.3     ; short-range electrostatic cutoff (in
nm)
rvdw                    = 333.3     ; short-range van der Waals cutoff (in
nm)
DispCorr                = EnerPres  ; account for cut-off vdW scheme
; Electrostatics
coulombtype             = cutoff    ; cutoff treatment
; Temperature coupling is on
tcoupl                  = andersen  ; Andersen thermostat
tc-grps                 = System    ; couple system to bath
tau_t                   = 0.1       ; time constant, in ps
ref_t                   = 300       ; reference temperature, one for each
group, in K
nstcomm                 = 1
; 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                = 300       ; temperature for Maxwell distribution
gen_seed                = -1        ; generate a random seed

=====================================================================

Kindly, Lazaro

--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================

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