[gmx-users] Freezing a portion of a protein during simulation
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 29 13:57:37 CEST 2010
Anirban Ghosh wrote:
> Hello Justin,
>
> Thanks a lot for your reply.
> I am using the option "freezegrps" in my .mdp file, given below:
> -----------------------------------------------------------------------------------------------------------------------------------------
>
> ;define = -DSTRONG_POSRES
> define = -DPOSRES ; position restrain the protein
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 10000 ; 2 * 50000 = 100 ps
> dt = 0.002 ; 2 fs
> ; Output control
> nstxout = 100 ; save coordinates every 0.2 ps
> nstvout = 100 ; save velocities every 0.2 ps
> nstenergy = 100 ; save energies every 0.2 ps
> nstlog = 100 ; update log file every 0.2 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
> ns_type = grid ; search neighboring grid cels
> 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 = 300 300 ; 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 = 300 ; temperature for Maxwell distribution
> gen_seed = -1 ; generate a random seed
>
> freezegrps = Fixed
> freezedim = Y Y Y
> --------------------------------------------------------------------------------------------------------------------------------------------
>
> I was just wondering how to give the "energygrp_excl" parameters with
> it. Can you please guide me regarding this and also please go through
> the other parameters in the .mdp file.
>
If you're using freezegrps, I see no need to define position restraints.
As for the exclusions, your group "Fixed" has to be listed in energygrps, and
exclusions within this group are established with "energygrp_excl = Fixed
Fixed." There are a whole host of errors that can come up, based on what
exactly "Fixed" comprises, but there are some good threads in the archives on
how to fix these. I still think using position restraints is far easier...
-Justin
> Regards,
>
> Anirban
>
>
>
>
>
>
>
> On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Anirban Ghosh wrote:
>
> Hello Justin,
>
> In my topology file I am declaring:
> ---------------------------------------------------------------------------------------------------------------
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Strong position restraints on rest of B2AR
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
>
>
> What is in strong_posre.itp? Presumably you're only restraining
> certain residues, right? Did you create this with genrestr and an
> appropriate index group?
>
>
> ; Include water topology
> #include "spc.itp"
> -----------------------------------------------------------------------------------------------------------------
> And in my .mdp file I am giving:
> -----------------------------------------------------------------------------------------------------------------
> define = -DSTRONG_POSRES ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 5000 ; 2 * 50000 = 100 ps
> dt = 0.002 ; 2 fs
> -------------------------------------------------------------------------------------------------------------------
>
>
> If this is the entirety of your .mdp file, you're asking for
> trouble. Allowing all other parameters to be taken as default is
> very dangerous, and probably inappropriate (most notably cutoff
> electrostatics).
>
>
> But now what I am getting is that if I run MD using these
> restraints on the helical portion of the protein, then I am
> getting LINCS errors. However, if I allow the entire protein to
> move during MD, then it is running fine. What mistake am I
> making? And how can I freeze properly the helical portions and
> simulate only the loop? Thanks a lot in advance.
>
>
> Recognize that there is a difference between "freezing" and
> "restraining." Read in the manual about what freezing is versus
> position restraints. Either way, you should be able to get things
> up and running, but position restraints are a bit easier to implement.
>
> If an unrestrained simulation runs fine (using that fragmented .mdp
> file?) then there are probably just bad clashes in the system that
> the restraints are not allowing to relax.
>
> -Justin
>
> Regards,
>
> Anirban
>
>
> On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Anirban Ghosh wrote:
>
> Hi ALL,
>
> I want to do a MD simulation by restraining (freezing) the
> helical portions and allowing only the loop regions to
> move. I
> tried doing this by applying heavy restrain on the helical
> residues by generating a .itp file with the "genrestr"
> command
> with an index file containing the desired residue numbers.
> However during the simulation I am finding that the entire
> protein is moving. Am I doing anything wrong? Or is there any
> other way to freeze a portion of a protein? Any suggestion is
> welcome. thanks a lot in advance.
>
>
> If your protein is still moving, then you aren't correctly
> applying
> your position restraints. Without seeing your topology and .mdp
> file, there's no way to know what you're doing wrong.
>
> You can also use the freezegrps option in the .mdp file, but then
> you also have to make sure you're using the appropriate
> energygrp_excl, etc. It is generally much easier to apply
> position
> restraints.
>
> -Justin
>
>
> Regards,
>
> Anirban
>
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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