[gmx-users] How to prevent velocity generation for my position restrained molecules ?

[Justin Lemkul]

On 4/14/20 5:48 PM, Mohamed Abdelaal wrote:
> Hello everybody,
>
> I am simulating the evaporation process for different atoms on a graphene
> sheet and the z-coordinate of each graphene carbon atom was restrained
> (using position restrain).
>
> The energy minimization was successfully done without any errors
>
> Then I started the equilibration, I have done the NVT. My nvt.mdp file
> is written below. I have added the -DPOSRES to enable the position
> restrain and I added temperature
>
>   coupling for both the GRM (the graphene sheet molecules) and the G8LE
> (The residue molecules; the molecules I am evaporating) then I wrote
> generate velocity = yes.
>
> After finishing the NVT  equilibration, I checked the nvt.gro file and
> the problem now is that, I have velocity for both the graphene
> molecules (which supposed to be position
>
> restrained) and for the residue. How can I generate velocity for the
> residue only (G8LE) and make sure that the graphene sheet is
> restrained.
>

Applying restraints does not prevent dynamics; your restrained atoms 
will have velocities. There will be a "Position Rest." term written to 
the .log and .edr files that is a clear signal your restraints were on 
and working.

If you want the group completely frozen (no position or velocity 
updates), that's what freezegrps is for, but freezing anything is highly 
artificial.

-Justin

> title                   =  NVT equilibration
> define                  = -DPOSRES  ; position restrain the protein
> ; Run parameters
> integrator              = md        ; leap-frog integrator
> nsteps                  = 50000     ; 2 * 50000 = 100 ps
> dt                      = 0.0005     ; 0.5 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 all-angles
> cutoff-scheme           = Verlet    ; Buffered neighbor searching
> ns_type                 = grid      ; search neighboring grid cells
> nstlist                 = 10        ; 20 fs, largely irrelevant with Verlet
> rcoulomb                = 1.0       ; short-range electrostatic cutoff (in nm)
> rvdw                    = 1.0       ; short-range van der Waals cutoff (in nm)
> DispCorr                = EnerPres  ; account for cut-off vdW scheme
> ; Electrostatics
> coulombtype             = cut-off   ; Particle Mesh Ewald for
> long-range electrostatics
> pme_order               = 4         ; cubic interpolation
> fourierspacing          = 0.16      ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl                  = V-rescale             ; modified Berendsen thermostat
> tc-grps                 = G8LE GRM  ; 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 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
> periodic_molecules = yes
>
>
> Many thanks,
>
> Mohamed

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

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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