Thank you Mark for the suggestion!
-Mensaje original-
De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] En nombre de Mark
Abraham
Enviado el: jueves, 12 de julio de 2018 19:01
Para: gmx-us...@gromacs.org
CC: gromacs.org_gmx-users@maillist.sys.kth.se
Asunto: Re: [gmx-users] Fatal error: Invalid T coupling input: 0 groups, 1
ref-t values and 1 tau-t values
Hi,
You need to specify a group, eg System. That this is not the default behavior
protects you from making a typo and accidentally coupling the whole system when
it was not your intent.
Mark
On Thu, Jul 12, 2018, 17:24 Gonzalez Fernandez, Cristina <
cristina.gonzalezf...@unican.es> wrote:
> Dear Gromacs users,
>
> I am trying to perform a NVT equilibration. However, I obtain this error:
>
> Fatal error:
> Invalid T coupling input: 0 groups, 1 ref-t values and 1 tau-t values
>
> I don't understand the problem because I don't have defined any group,
> I am indicating the ref-t and tau-t for the whole system.
>
> My .mdp file is:
>
> define = -DPOSRES ; position restrain the lipid
>
> ; Run parameters
> integrator = md; leap-frog integrator
> nsteps = 5 ; 2 * 5 = 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 = all-bonds ; all bonds (even heavy atom-H
> bonds) constrained
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
>
> ; Neighborsearching
> cutoff-scheme = Verlet
> ns_type = grid ; search neighboring grid cells
> nstlist = 10; 20 fs, largely irrelevant with
> Verlet
> rcoulomb= 1.2 ; short-range electrostatic cutoff
> (in nm)
> rvdw= 1.2 ; short-range van der Waals cutoff
> (in nm)
>
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
>
> ; Temperature coupling is on
> tcoupl = nose-hoover ; nose-hoover thermostat
> 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
>
> ; Dispersion correction
> DispCorr= EnerPres ; account for cut-off vdW scheme
>
> ; Velocity generation
> gen_vel = yes ; assign velocities from Maxwell
> distribution
> gen_temp= 298 ; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
>
>
> Could anyone help me?
>
> Thank you in advance,
> C.
>
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