[gmx-users] Error in NVT equilibration

[Justin Lemkul]

On 9/24/18 6:46 AM, Gonzalez Fernandez, Cristina wrote:
> Hi Justin,
>
>
> Thank you very much for your suggestions, I ran the equilibration!
>
>
> After running the equilibration, I tabulated the temperature with time, and at time=0 the temperature is 277.73 K and at time=1ps the temperature is 294.03. The initial temperature is enough similar (I think) to the considered one. However, the temperature at 1ps is lower than the stated one (298K) in the annealing settings (and therefore at 0.134 ps the temperature is lower than 294 K instead of 298K).
>

You can't expect that the temperature will be dead-on at the instant you 
request it. You're warming very fast, to the point that I really don't 
understand the purpose of such a procedure. As with anything 
temperature-related, you have to allow time for the system and 
thermostat to respond to any change. I'd say your results are about as 
good as you can hope for.

> I copy the .mdp file in case you can detect the errors in this file, as I have been looking for the annealing settings in the GROMACS manual and in previous posts and I don't find what is wrong.
>
>
> title                   = Lipid NVT equilibration
> define                  = -DPOSRES  ; position restrain the lipid
> ; Run parameters
> integrator              = md        ; leap-frog integrator
> 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             = 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                = 1.4       ; short-range electrostatic cutoff (in nm)
> rvdw                    = 1.4       ; short-range van der Waals cutoff (in nm)
> DispCorr                = EnerPres  ; account for cut-off vdW scheme
> vdwtype                 = Cut-off
> vdw_modifier            = Potential-shift-Verlet
> 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
> coulomb_modifier        = Potential-shift-Verlet
> ; 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                = 278       ; temperature for Maxwell distribution
> gen_seed                = -1        ; generate a random seed
> ;Simulated annealing
> annealing               = single
> annealing_npoints       = 2
> annealing_time          = 0 0.134
> annealing_temp          = 278 298
>
>
>
> If I have understood correctly from previous posts, gen_temp must be equal to the lower annealing temperature (in this case 278K) and the ref_t must be equal to the highest annealing temperature (in this case 298 K), is it correct?

gen_temp should be the temperature at which you want to start the 
simulation. ref_t is ignored entirely when using annealing options.

-Justin

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

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