[gmx-users] position restraints

[Irem Altan]

Hi,

The .mdp file is as follows:

title           = OPLS Lysozyme NVT equilibration
define          = -DPOSRES	; position restrain the protein
; Run parameters
integrator	= md            ; leap-frog integrator
nsteps          = 50000000              ; 2 * 50000 = 10 ns
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 5000          ; save coordinates every 10 ps
nstvout         = 5000          ; save velocities every 10 ps
nstxtcout	= 5000
nstenergy	= 5000          ; save energies every 10 ps
nstlog          = 5000          ; update log file every 10 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        ;NEED TO RUN ON GPU
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0           ; 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          = 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           = 277   277     ; 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        = 277           ; temperature for Maxwell distribution
gen_seed        = -1            ; generate a random seed


However, it would be much better if I could freeze the protein atoms completely. How could I modify this .mdp file to do that? Also, I first do energy minimization. Do I need to freeze the protein atoms in the minimization .mdp file as well? Below are the contents of this file:

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator	= steep         ; Algorithm (steep = steepest descent minimization)
emtol           = 1000.0        ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep          = 0.00001          ; Energy step size
nsteps          = 50000         ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist         = 1             ; Frequency to update the neighbor list and long range forces
ns_type         = grid          ; Method to determine neighbor list (simple, grid)
rlist           = 1.0           ; Cut-off for making neighbor list (short range forces)
coulombtype     = PME           ; Treatment of long range electrostatic interactions
rcoulomb        = 1.0           ; Short-range electrostatic cut-off
rvdw            = 1.0           ; Short-range Van der Waals cut-off
pbc             = xyz           ; Periodic Boundary Conditions (yes/no)

Best,
Irem

> On Apr 4, 2016, at 1:36 PM, Christopher Neale <chris.neale at alum.utoronto.ca> wrote:
> 
> What did you set for refcoord-scaling ? How are you treating volume/pressure? Please post a full .mdp file. If you want, you can simply fix the positions and not let them move at all with freezegrps etc.
> 
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Irem Altan <irem.altan at duke.edu>
> Sent: 04 April 2016 10:23
> To: gmx-users at gromacs.org
> Subject: [gmx-users] position restraints
> 
> Hi,
> 
> I have a simulation in which I want to keep the protein coordinates fixed. I have tried using force constraints of strength 1000, 5000, and 10000. With 5000, there are about 100-150 atoms (out of ~1700) that drift more than 0.4A away from their equilibrium positions. This number increases when I use 10000. Is this expected behavior? What can I do to prevent the equilibrium positions from drifting away more than 0.4A?
> 
> Best,
> Irem
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