[gmx-users] Freezing a portion of a protein during simulation

Anirban Ghosh reach.anirban.ghosh at gmail.com
Thu Apr 29 08:47:03 CEST 2010


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.

Regards,

Anirban






On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul <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>> 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> | (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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