Acoot Brett wrote:
Dear All,
The first mini.mdp is as following:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0 ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to
perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and
long range forces
ns_type = grid ; Method to determine neighbor list (simple,
grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range
forces)
coulombtype = PME ; Treatment of long range electrostatic
interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
The second mini.mdp is as folowing:
; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range
forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.4 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.4 ; Short-range electrostatic cut-off
rvdw = 1.4 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions
The difference is the cut-off. One is 1.4,the other is 1.0. Can anyone explain
their difference on the influence of the MD result?
You should be able to see this yourself from the resulting structure and
energetic terms. I'd suspect for simple energy minimization (which, by
definition, is not MD) the differences will be rather small. An actual MD
simulation, however, may be influenced significantly.
Suppose I use AMBER 99SB force field, will you lease tell me how can decide the
value of the above cut-offs?
By reading the primary reference for the force field to understand the
conditions for which it was parameterized, then any subsequent tests of the
force field that may have discovered improvements. Researching a force field
and its proper implementation can often be the most time-consuming part of
preparing your simulations, but it's better to spend a few days reading and
searching than a few weeks or months generating junk data because your setup is
wrong ;)
-Justin
--
========================================
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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