[gmx-users] Md continuation with cpt
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 27 17:18:51 CEST 2011
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.
> 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)
> 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?
> Many thanks in advance and best regards
> 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: amarabotti at isa.cnr.it <mailto:amarabotti at 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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