[gmx-users] about error running temperature equilibration

[Justin Lemkul]

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

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

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