[gmx-users] constraint pull code / gromacs 5.0.4
CARDELLINI ANNALISA
d021974 at polito.it
Tue Jun 23 19:53:13 CEST 2015
Dear gromacs users,
I'm using the pull code to evaluate the Potential of Mean
Forces between two nanoparticles(NPs) of Radius = 1nm.
Specifically, in order to create the configurations
(i.e.the 2 NPs at different centr of mass distance) I used
the constraint pull code.
Then for each configuration I run a simulation of 2ns.
Part of the mdp file that I used is:
...
; 9) NEIGHBOR SEARCHING
; cut-off scheme
cutoff-scheme = Verlet
nstlist = 10 ;
ns_type = grid
pbc = xyz
periodic_molecules = yes
rlist = 1.3 ;
; 10) ELECTROSTATICS
coulombtype = PME-Switch ;
pme_order = 4
rcoulomb = 1.3 ;
rcoulomb-switch = 1.25 ;
; 11) VdW
vdw-type = Cut-off ;
rvdw-switch = 1.3 ;
rvdw = 1.3
DispCorr = EnerPres ;
; 13) EWALD
fourierspacing = 0.12 ; (0.12) [nm] default
fourier_nx = 0 ; (0) default
fourier_ny = 0 ; (0) default
fourier_nz = 0 ; (0) default
ewald_rtol = 1e-5 ; (1e-5) default
optimize_fft = yes
; 14) TEMPERATURE COUPLING
Tcoupl = Nose-Hoover
tc_grps = UNK SOL
tau_t = 0.1 0.1
ref_t = 300 300
; 15) PRESSURE COUPLING
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 2 2 ; (1) [ps] default
compressibility = 4.5e-5 4.5e-5 ; [bar-1]
ref_p = 1 1 ; [bar]
refcoord_scaling = com ;
; 17) VELOCITY GENERATION
gen-vel = no
gen-temp = 300
gen-seed = -1
; 18) BONDS
constraints = ; convert all bonds to
constraints
constraint_algorithm = ; LINear Constraint Solver
continuation = yes ;
lincs_order = 4 ;
lincs_iter = 1 ;
lincs_warnangle = 90 ;
; Pull type:
pull = constraint ;
pull-geometry = distance ;
pull-dim = Y N N ;
pull-start = yes ;
pull-ngroups = 2 ;
pull-group1-name = 1UNK ;
pull-group2-name = 2UNK
pull-coord1-groups = 1 2
pull-coord1-rate = 0.0 ;
0.01 nm per ps
pull-nstxout = 1000 ; every 2 ps
pull-nstfout = 1000 ; every 2 ps
pull-coord1-init = 0.0 ;
My problem is related to the resulting forces that I
obtained. They do not seem to converge and they are really
fluactuating for any configuration (i.e. indipendently
from the com distance)
An example of pullf.xvg that I obtained at 2 nm com
distance
..
1992.5000 -2367.46
1993.0000 -6738.59
1993.5000 361.472
1994.0000 647.644
1994.5000 -6222.61
1995.0000 6018.37
1995.5000 1921.95
1996.0000 -1618.72
1996.5000 1279.2
1997.0000 1302.08
1997.5000 2256.82
1998.0000 1485.05
1998.5000 2318.51
1999.0000 -3588.26
1999.5000 979.835
2000.0000 -678.607
Of course, the PMF that I got with a simple intagration of
the forces is characterized by enormous error bars and its
shape does not have any sense.
Do you have some suggestions for getting converged forces?
Do you see some errors in the mdp file?
Thank you in advance for your help.
Annalisa
Annalisa Cardellini, M.Sc.
Ph.D. student
Politecnico di Torino - Energy Department
Corso Duca degli Abruzzi, 24
10129 Turin - ITALY
Tel: +39-011-090-4495
Fax: +39-011-090-4499
E-mail: annalisa.cardellini at polito.it
SMaLL: http://www.polito.it/small
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