On 6/4/13 12:51 PM, tarak karmakar wrote:
Yeah!
It is indeed a silly point to generate a velocity distribution at 0 K. (
Maxwell-Boltzmann will be in trouble)
After the warm up, now let say my protein is in 300 K, can't I generate a
velocity distribution at 300 k (using the keyword gen_vel = yes, gen_temp =
300 K gen_seed = 173529 ) during my production run?
You can generate velocities whenever you like, but you'll have to allow for some
time to equilibrate, so what you're calling "production" isn't entirely
production because it's no longer equilibrated in any real sense. The heating
phase may help to optimize the initial geometry, but regenerating velocities may
screw everything up if something becomes unstable. Assuming restraints are off
during "production," then you can screw up the geometry of your system if
something gets an unpleasant kick from the new velocities.
-Justin
On Tue, Jun 4, 2013 at 10:10 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 6/4/13 12:17 PM, tarak karmakar wrote:
Thanks Justin.
Sorry for not uploading the full .mdp. Here it is,
; 7.3.3 Run Control
integrator = md
tinit = 0
dt = 0.001
nsteps = 5000000
nstcomm = 1
comm_grps = system
comm_mode = linear
energygrps = system
; 7.3.8 Output Control
nstxout = 5000
nstfout = 5000
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
xtc_precision = 1000
xtc_grps = System
; 7.3.9 Neighbor Searching
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
rlistlong = 1.4
; 7.3.10 Electrostatics
coulombtype = PME
rcoulomb = 1.2
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
; 7.3.11 VdW
vdwtype = switch
rvdw = 1.2
rvdw-switch = 1.0
DispCorr = Ener
; 7.3.14 Temperature Coupling
tcoupl = nose-hoover
tc_grps = system
tau_t = 1.0
ref_t = 300
; 7.3.15 Pressure Coupling
pcoupl = parrinello-rahman
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 93873959697
; 7.3.18 Bonds
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
lincs_order = 4
lincs_iter = 1
lincs_warnangle = 30
Note: Using CHARMM27 force field
I didn't use the 'continuation' part here.
In the heating run I didn't put any constraints but in the production MD,
I
do apply constraints to the covalent bonds involving hydrogens. I just
want
The introduction of constraints explains the observed behavior. You ran
an unconstrained simulation, then at step 0 of the constrained simulation,
the constraints have to be satisfied, which may introduce sudden movement
in atomic positions, hence large velocities and a high temperature. The
rule of thumb I always use - if you're going to use constraints during
production simulations, use constraints during equilibration. I have seen
several instances where unconstrained equilibration causes constrained
simulations to later fail.
to test the ligand movement inside the protein cavity in different set of
initial velocities to get the feelings of how ligand is interacting with
certain residues.
So, then should I use these different velocity generating seeds during the
warm up step?
That's an interesting question. If you're warming from 0 -> 300 K, I
don't know how grompp will generate velocities at 0 K, but regenerating
velocities after warming seems to defeat the purpose of doing the warming
at all, in my mind, since you're just going to re-randomize the entire
system by doing so.
-Justin
--
==============================**==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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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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