On 6/13/12 7:55 AM, [email protected] wrote:
Hi!
Thank you for your answer.
On 13/06/2012 6:44 PM, [email protected]
wrote:
Hi everybody,
I want to do a minimization of the hydrogens of my protein. Only the
hydrogens.
Doesn't really matter - nothing will move more than a fraction of an
Angstrom unless it's horribly wrong, in which case not moving the heavy
atoms won't help you.
And I want to do this with implicit solvent.
Probably not worth the effort if you're just preparing for MD.
Our goal is not an MD simulation of the protein. We plan a
Poisson-Boltzmann electrostatics calculation. For that we need the heavy
atoms as they are in the crystal structure (even 1 Angstroem movement
would be too much) with good hydrogen atom position.
With restraints on heavy atoms, your positions will not deviate very much
at
all. A 1 Angstrom movement would be huge in this case; I would expect
your
deviations to be orders of magnitude less.
We need to minimize, simulate, minimize, simulate the hydrogen atoms.
I don't follow the logic here. You say you need to do an EM of the H
atoms in
order to do some PBSA calculation with no MD, but here you're doing two
iterations of EM and MD.
Implicit solvent is ok for us. (For a later MD run of the complete
protein, we will use explicit solvent).
This is the .mdp file:
There are several problems here, most of which I've already stated, but
I'll
recapitulate them again.
define = -DPOSRES
constraints = all-bonds
integrator = steep
nsteps = 30000
vdwtype = cutoff
coulombtype = cutoff
As Mark said, these settings should be "cut-off" not "cutoff."
epsilon_rf = 0
pbc = xyz
For an implicit system, periodicity should be set to "no" and grompp will
warn
you about using angular COM removal (invoked below) if you leave it set as
is.
nstlist = 1
ns_type = grid
rlist = 1
rcoulomb = 1.2
rvdw = 1.2
Finite cutoffs with implicit solvent will lead to instability and poor
energy
conservation. These three lines (rlist, rcoulomb, rvdw) should be set to
zero,
unless you're satisfied with artifacts.
rvdw_switch = 0.7
This setting has no effect when using cutoffs.
comm-mode = angular
comm-grps = System
nstcgsteep = 1000
emtol = 5.0
Unless you've compiled with double precision, it is unlikely you will
achieve a
minimal force this low. The use of restraints is going to preclude most
movement in the system, so don't be surprised if grompp does not (and
cannot)
achieve this tolerance.
emstep = 0.01
implicit_solvent = GBSA
gb_algorithm = HCT
nstgbradii = 1
rgbradii = 1
This should also be set to zero if the above neighbor searching parameters
are zero.
gb_epsilon_solvent = 80
gb_saltconc = 0
sa_algorithm = Ace-approximation
sa_surface_tension = -1
Additionally I have a question according to the vdwtype and coulombtype.
Why do I have to set the two parameters to cutoff?
Because settings like PME don't make sense for implicit solvent
calculations.
Plain cutoffs with finite values are almost never adequate for any
purpose, however.
-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
========================================
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