[gmx-users] Same starting structure but different trajectories
Emanuel.Peter at chemie.uni-regensburg.de
Wed Feb 17 09:24:47 CET 2010
Dear Gromacs users,
At the moment I have some doubt on my run input .mdp file.
I simulated a protein structure in water and I used parameters as following in my mdp file:
title = MD simulation of xxx
cpp = /lib/cpp
;Directories to include in the topology format
include = -I../top
integrator = md
dt = 0.001
nsteps = 1000000
nstxout = 10000
;frequency to write velocities to output trajectory file
nstvout = 10000
;frequency to write energies to log file
nstlog = 10000
;frequency to write energies to energy file
nstenergy = 10000
;frequency to write coordinates to xtc trajectory
nstxtcout = 10000
;group(s) to write to xtc trajectory
xtc_grps = prot sol XXX
group(s) to write to energy file
energygrps = prot sol XXX
;Frequency to update the neighbor list (and the long-range forces,
;when using twin-range cut-off's).
nstlist = 10
;Make a grid in the box and only check atoms in neighboring grid cells
;when constructing a new neighbor list every nstlist steps.
ns_type = grid
;cut-off distance for the short-range neighbor list
rlist = 1.4
;treatment of electrostatic interactions
coulombtype = PME
fourierspacing = 0.12
pme_order = 4
rcoulomb = 1.4
;treatment of van der waals interactions
rvdw = 1.4
; Periodic boudary conditions in all the directions
pbc = xyz
tcoupl = nose-hoover
tc-grps = protein NA+ CFP SOL
tau_t = 0.1 0.1 0.1 0.1
ref_t = 300 300 300 300
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 173529
constraints = none
My problem is as following:
I have simulated the protein with exactly the same starting structure, the same electrostatics, the same
seed for velocity generation and the same thermostating scheme three times, but I did not get exactly the same trajectory.
I took the following measurement for comparing my trajectories:
g_mindist -f traj.trr -s input.tpr -n index_atom1_atom2.ndx -od dist_atom1_atom2.xvg
The atomic distances always differ from each other by 0.1 to 0.3 angstrom whereas the starting value at t=0 is the same.
Could you tell me why I get in three different simulations with 3 totally equivalent inputs three different trajectories?
In my opinion it should give 3 times a identical trajectory.
Thank you in advance.
More information about the gromacs.org_gmx-users