[gmx-users] position restraints
Christopher Neale
chris.neale at alum.utoronto.ca
Mon Apr 4 23:21:52 CEST 2016
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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