Please keep the discussion on the mailing list.
On 5/14/13 11:37 PM, Tong Li wrote:
Hi Justin,
Really appreciate your prompt reply! I got the inconsistence, the atom index in
the original tpr file is different with the ones in xtc result file. However, I
have no ideas what caused this… Some atoms are not in the ‘tpr’ file, but appear
in the traj file (xtc) and also in the output geometry file (gro).
This is impossible. If atoms are not in a .tpr file, they can't be written to
configurations and trajectories. Have you mixed up any of your files? Use of
gmxcheck and gmxdump will clarify what you have in what file.
-Justin
I was using absolute implicit solvent simulation, never used any or deduct any
water molecules from the simulation system. From geometry optimization, to nvt
relaxation, then steered MD simulation in nvt assemble.
Thanks a lot for your kind help!
Cheers,
Tong
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = cut-off
rcoulomb = 1.2
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 2
epsilon_rf = 0
; Method for doing Van der Waals
vdw-type = cut-off
; cut-off lengths
rvdw = 1.2
; Temperature coupling is on
tcoupl = Berendsen ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 310 310 ; reference temperature, one
for each group, in K
implicit-solvent = GBSA
algorithm = HCT
rgbradii = 1.2
; pull code
pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = yes
pull_ngroups = 1
pull_group0 = non-Protein
pull_group1 = Protein
pull_init1 = 0
pull_rate1 = -2
pull_k1 = 2000 ; kJ mol^-1 nm^-2
pull_nstxout = 100 ; every 0.2 ps
pull_nstfout = 100 ; every 0.2 ps
--
========================================
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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