On 12/12/12 5:15 PM, Davide Mercadante wrote:
Dear Justin,
Thank you for your reply. To be sure I carefully ran the simulations again
using the following .mdp file that includes the pull lines and
-DPOSRES_B to restrain chain B from being pulled when chain A is being
pulled (it is the .mdp file given in the tutorial):
title = Umbrella pulling simulation
define = -DPOSRES_B
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 250000 ; 500 ps
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = Nose-Hoover
tc_grps = Protein Non-Protein
tau_t = 0.5 0.5
ref_t = 310 310
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Pull code
pull = umbrella
pull_geometry = distance ; simple distance increase
pull_dim = N N Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = Chain_B
pull_group1 = Chain_A
pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
I get slightly different distances but it is still now working. From the
load of the trajectories chain B is not getting pulled. However, after
I'm assuming you mean chain A here. Chain B is restrained while A is pulled
away from it.
running the distance.pl script I get a COM distance within the range 2.3nm
to 6.0nm). Can you please help me to understand what I am doing wrong?
None of this makes sense to me. Your COM distance increases, but you say you
can't see anything moving? One necessitates the other. Are you loading the
trajectory properly? If you're using VMD, you have to load the starting
coordinates first and then the trajectory is loaded as data for that molecule.
My command line is:
Grompp -f pull.mdp -c after_npt.gro -p topol.top -o pull.tpr -t state.cpt
(checkpoint file from the previous npt step) -n index.ndx (which includes
groups 19 and 20, chains A and B respectively).
Mdrun then uses pull.tpr...
Please don't hesitate to ask me any other information you may need to
figure this out. I am not sure what I am doing wrong..
If you still can't figure out what's going on, please send me (off list) the
following:
1. Your summary_distances.txt file
2. Several coordinate files - conf0.gro, conf100.gro, conf200.gro, and
conf500.gro
-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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