[gmx-users] Md continuation with cpt

Anna Marabotti anna.marabotti at isa.cnr.it
Wed Apr 27 17:03:44 CEST 2011

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
init_step = 70000 (the last step after NVT+NPT)
tinit = 0
nstxout,vout,fout,log,energy: 50000
In the command to launch the MD simulation I set:
mpirun -np 32 -s 1R3Afull.tpr -deffnm 1R3Afull -cpt 60
After the first 5 ns of simulation, I obtained all the files expected, and I
extended the trajectory of further 5 ns using the command:
tpbconv -s 1R3Afull.tpr -extend 5000 -o 1R3Afull2.tpr
mpirun -np 32 -s 1R3Afull2.tpr -cpi 1R3Afull.cpt -deffnm 1R3Afull2 -cpt 60
I repeated the procedure until I obtained 20 ns trajectory.
Then, I used trjcat to concatenate 1R3Afull.xtc + 1R3Afull2.xtc +
1R3Afull3.xtc + 1R3Afull4.xtc creating 1R3Afull20ns.xtc and eneconv to do
the same with 1R3Afull.edr + 1R3Afull2.edr + 1R3Afull3.edr + 1R3Afull4.edr,
creating 1R3Afull20ns.edr. Then, I used gmxcheck -e 1R3Afull20ns.edr to
check the final .edr file. I obtained an error message:
Checking energy file 1R3Afull20ns.edr
Opened 1R3Afull20ns.edr as double precision energy file
frame:      0 (index      0), t:    140.000         
Reading energy frame      2 time  300.000           
Timesteps at t=200 don't match (60, 100)
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            
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?
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
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)
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