[gmx-users] Freezing a portion of a protein during simulation
Anirban Ghosh
reach.anirban.ghosh at gmail.com
Thu Apr 29 12:13:15 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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