[gmx-users] Problem while running equilibration

[Alessandra Villa]

Hi,
see some comments/suggestions below.
Best regards
Alessandra

On Fri, Jan 17, 2020 at 8:34 AM Nirali Desai <nirali.d.imsc14 at ahduni.edu.in>
wrote:

> Dear all,
>
> My system consists of a three chains of protein: PROA, PROB and PROCLIG
> (with ligand).
> Minimization is running properly without any error.
> Parameters used are:
> title = Minimization ; Title of run
> define          = -DPOSRES
>
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000   ; Stop minimization when the maximum force < 10.0 kJ/mol
> emstep      = 0.01      ; Energy step size
> nsteps = 50000   ; Maximum number of (minimization) steps to perform
> energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk
> energygrp_excl  = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB
> SOL
> freezegrps      = PROCLIG
> freezedim       = Y Y Y
>
> But, while running equilibration it is giving error of the blowing up of
> the system like water molecule not settled, clashes etc.
> I ran the equilibration without adding water and also without using freeze
> groups. It is running perfectly. I turned off constraints and pressure
> coupling while using freezegroups.
>  Parameters used:
>
> title       = Protein-ligand complex NVT equilibration
> define      = -DPOSRES  ; position restrain the protein and ligand
>


> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 50000     ; 2 * 50000 = 100 ps
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout     = 100       ; save coordinates every 0.2 ps
> nstvout     = 100       ; save velocities every 0.2 ps
> nstenergy   = 100       ; save energies every 0.2 ps
> nstlog      = 100       ; update log file every 0.2 ps
> energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk
> energygrp_excl  = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB
> SOL
>

Why do you use energygrp_excl ?   Usually  energygrp_excl are useful for
speeding up energy calculations with mdrun -rerun and for excluding
interactions within frozen groups (in your case only PROCLIG)

freezegrps      = PROCLIG
> freezedim       = Y Y Y
>

Do you need to freeze group?
You already have position restrains on protein and ligand



> ; Bond parameters
> continuation    = no            ; first dynamics run
> constraints     = none     ; all bonds (even heavy atom-H bonds)
> constrained
>

You are using 2fs and atomistic force field, then you need at least h-bond
to be constrained



> ; Neighborsearching
> ns_type     = grid      ; search neighboring grid cells
> cutoff-scheme  = group
> nstlist     = 20         ; 10 fs
> rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
> rvdw        = 0.9       ; 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
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = Protein non-protein   ; two coupling groups - more accurate
> tau_t       = 0.1   0.1                     ; time constant, in ps
> ref_t       = 300   300                     ; reference temperature, one
> for each group, in K
> ; Pressure coupling
> 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    = 300       ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed
>
> Please guide me on this.
> If you have any suggestions I will really appreciate.
>
> Thanks and regards,
> Nirali
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