[gmx-users] position restraints

Irem Altan irem.altan at duke.edu
Mon Apr 4 22:28:22 CEST 2016


I did, and I have a more specific question: what options do I have for specifying freeze groups? Right now I’m trying Protein-H. I also have a specific kind of ion that I’d like to freeze. The energy minimization step fails, as GROMACS complains that it can’t settle a water molecule (which is nowhere near the protein). However, the MD simulation seems to be running, after doing the minimization with just position restraints. Is this expected behavior?

Best,
Irem

> On Apr 4, 2016, at 4:23 PM, Christopher Neale <chris.neale at alum.utoronto.ca> wrote:
> 
> Check the manual for freezegrps ?
> 
> _______________________________________
> 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 15:54
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] position restraints
> 
> 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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