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 <[email protected]
<mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> 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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