[gmx-users] Re: single point calculation with gromacs
fantasticqhl
fantasticqhl at gmail.com
Thu Oct 31 09:48:47 CET 2013
Dear Justin,
*Thanks very much for your reply! Here is my minim.mdp I used:*
/; 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 = 0 ; 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 = simple ; Method to determine neighbor list
(simple, grid)
rlist = 9.0 ; Cut-off for making neighbor list (short
range forces)
coulombtype = Cut-off ; Treatment of long range
electrostatic interactions
rcoulomb = 9.0 ; Short-range electrostatic cut-off
rvdw = 9.0 ; Short-range Van der Waals cut-off
pbc = no ; Periodic Boundary Conditions (yes/no)
/
*If I used this mdp file for 0-step minimization, I could get potential
energy around 700 kJ/mol for my system. But I would get potential energy
around 2.6e+05 kJ/mol if I used the mdv.mdp (md simulation in vacuum) for
calculations with rerun option. And the bond potential could also reach as
high as 1.1e+05 kJ/mol. Actually, my system is very small, it contains only
37 atoms. I believe that the energy reported by 0-step minimization were
more reasonable. So I guess that there might be some problem for the mdp
file usd with rerun, and here is the mdv.mdp:*
/define = ;-DPOSRES
integrator = md ; molecular dynamics algorithm
tinit = 0.0 ; start time and timestep in ps
dt = 0.002 ; time step in ps
nsteps = 2 ; number of steps for 1000ns run
emtol = 100 ; convergence criterion
emstep = 0.05 ; intial step size
nstlist = 0 ; step frequency for updating neighbour list
ns_type = simple ; method for neighbour searching (?)
nstxout = 1 ; frequency for writing coords to output .trr
file
nstvout = 1 ; frequency for writing velocities to
output...should be same as nstxout
nstfout = 1 ; frequency for writing forces to output
nstlog = 1 ; frequency for writing energies to log file
nstenergy = 1 ; frequency for writing energies to energy
file
nstxtcout = 1 ; frequency for writing coords to xtc traj
xtc_grps = system ; group(s) whose coords are to be written in
xtc traj
energygrps = system ; group(s) whose energy is to be written in
energy file
pbc = no ; use pbc
rlist = 0 ; cutoff lengths (nm)
epsilon_r = 1.0 ; Dielectric constant (DC) for twin-range or
DC of reaction field
niter = 100 ; Some thingies for future use
fourierspacing = 0.16
fourier_nx = 30
fourier_ny = 30
fourier_nz = 30
coulombtype = Cut-off ; truncation for minimisation, with
large cutoff
rcoulomb = 0
rcoulomb-switch = 0
vdw-type = Cut-off ; truncation for minimisation, with
large cutoff
rvdw-switch = 0
rvdw = 0 ; cut-off lengths
epsilon_surface = 0
optimize_fft = yes
Tcoupl = V-rescale
tc_grps = system
tau_t = 0.01
ref_t = 300
Pcoupl = no ; Parrinello-Rahman ; Pressure coupling
gen_vel = yes
gen_temp = 300
gen_seed = -1
constraints = none ; OPTIONS FOR BOND CONSTRAINTS
constraint-algorithm = Lincs ; Type of constraint algorithm
lincs_order = 4 ;4 ; Highest order in the expansion
of the constraint coupling matrix
lincs_iter = 1
lincs_warnangle = 30 ; Lincs will write a warning to the stderr
if in one step a bond rotates
; over more degrees than
unconstrained-start = no ; Do not constrain the start configuration
;Shake-SOR = no ; Use successive overrelaxation to reduce
the number of shake iterations
;shake-tol = 1e-04 ; Relative tolerance of shake
morse = no ; Convert harmonic bonds to morse potentials
/
*Could you please have a check for me again? Thanks in advance!
All the best,
Qinghua*
--
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