[gmx-users] position restraints
Irem Altan
irem.altan at duke.edu
Mon Apr 4 23:57:34 CEST 2016
Thanks, I figured it out. (In case anyone wonders) the comma was not necessary:
freezegrps = Protein-H YB
freezedim = Y Y Y Y Y Y
> On Apr 4, 2016, at 5:51 PM, Christopher Neale <chris.neale at alum.utoronto.ca> wrote:
>
> 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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