[gmx-users] position restraints

Christopher Neale chris.neale at alum.utoronto.ca
Mon Apr 4 23:51:59 CEST 2016


I didn't use freezegrps in a long time, but I presume that you define a group in the .ndx file and then you use the name of that group.

________________________________________
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 17:39
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] position restraints

Thanks, it worked!

I couldn’t find anything in the documentation/manual as to how the groups to be freezed are named. For my case, I want to freeze the protein heavy atoms and ytterbium ions. In that case, would I do freezegrp = Protein-H, YB  and freezedim = Y Y Y Y Y Y?

Best,
Irem

> On Apr 4, 2016, at 5:21 PM, Christopher Neale <chris.neale at alum.utoronto.ca> wrote:
>
> I've never understood it, but when your system gets more complicated it is often necessary to use flexible water during minimization. define = -DFLEXIBLE for most water molecules. You can remove this for the MD, but it is for me sometimes necessary for EM.
>
> You have nearly unlimited options for the freeze group. What you freeze depends on what you want to do.
>
> ________________________________________
> 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 16:28
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] position restraints
>
> 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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