James Starlight wrote:
Justin,
I've forced with the problem that I could not prorerly minimized my
system in the NMA conditions. Even in STEEP minimizaation I could not
obtain Epot value lower than +3.00 with that parametries ( I've used
KALP peptide as a test input )
The Epot value is less significant than Fmax (which is what is set in the .mdp
file, anyway). What Fmax do you achieve? Real copied and pasted output would
be useful.
; Parameters describing what to do, when to stop and what to save
integrator = steep
emtol = 1 ; Stop minimization when the maximum force < 1.0
kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 5000000 ; 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 = 1.2 ; Cut-off for making neighbor list (short
range forces)
coulombtype = Shift
rcoulomb = 1.0
rcoulomb_switch = 0.0
vdwtype = Shift
rvdw = 1.0
rvdw_switch = 0.0
Than I've tried to futher minimized this structure via l-bfgs algorithm by
integrator = l-bfgs
dt = 0.01
emtol = 0.001 ;
emstep = 0.1 ; Energy step size
nsteps = 50000000 ; Maximum number of (minimization)
steps to perform
but Epot was still big.
What I've done wrong ?
Are you using single- or double-precision?
-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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
