Anna Marabotti wrote:
Dear gmx-users,
since I'm sending my simulations to a system with a queue with a
wallclock time of 24 h, I necessarily have to simulate small parts of my
simulation, that I "stick" together at the end with trjconv. To continue
my simulations, I'm using the .cpt file. Here my settings concerning the
number of steps, dt etc. Since I started the full MD after 20 ps NVT and
100 ps NPT I set the mdp file as:
integrator = md
dt = 0.002
nsteps = 2500000 (total 5 ns - the max time compatible with the
wallclock time)
init_step = 70000 (the last step after NVT+NPT)
Is it? 120 ps/0.002 ps = 60000 steps.
<snip>
Opened 1R3Afull20ns.edr as double precision energy file
frame: 0 (index 0), t: 140.000
Based on this output, frame 0 corresponds to a time of 140 ps, as set by your
init_step * dt.
Reading energy frame 2 time 300.000
Timesteps at t=200 don't match (60, 100)
It looks like the setting for nstenergy is causing frames to be written at
integral multiples of 100 ps, rather than init_step + nstenergy. So you have
frame 0 at 140 ps, frame 1 at 200 ps, then 100-ps intervals until...
Reading energy frame 50 time 5100.000
Timesteps at t=5100 don't match (100, 40)
etc.
Timesteps at t=5140 don't match (40, 60)
Timesteps at t=5200 don't match (60, 100)
Reading energy frame 100 time 10000.000
Timesteps at t=10100 don't match (100, 40)
Timesteps at t=10140 don't match (40, 60)
Timesteps at t=10200 don't match (60, 100)
Reading energy frame 150 time 14900.000
Timesteps at t=15100 don't match (100, 40)
Timesteps at t=15140 don't match (40, 60)
Timesteps at t=15200 don't match (60, 100)
Last energy frame read 198 time 19600.000
All of these mismatches seem to agree with the above theory. The difference is
always 40 or 60, the remainder of some break between your value determined by
init_step and initial time of 140 ps.
Found 199 frames.
gcq#131: "Royale With Cheese" (Pulp Fiction)
I don't understand why there are so many mismatches in my file. Moreover
all but one are in the correspondence of the "junctions" I made between
two consecutive 5 ns runs. Does it depend on some settings regarding
init_step or dt or tinit in the .mdp file? Did I make correctly the
continuation? Could somebody help me to find the error?
Is there some reason you needed the trajectory to start at 140 (120?) ps?
Usually a new trajectory is intitiated with init_step = 0. Continuing a run
using while still maintaining the previous ensemble does not necessarily need
init_step > 0.
It is possible this is a bug related to nst*out/energy/log being writing every
50000 steps and assuming init_step = 0 (i.e. writing at 100 ps rather than 240
ps, based on your initial settings). What version of Gromacs is this?
-Justin
Many thanks in advance and best regards
Anna
__________________________________________________________________
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: amarabo...@isa.cnr.it <mailto:amarabo...@isa.cnr.it>
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
"When a man with a gun meets a man with a pen, the man with the gun is a
dead man"
(Roberto Benigni, about Roberto Saviano)
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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