[gmx-users] Md continuation with cpt

[Anna Marabotti]

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)
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
 
and
 
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
 
__________________________________________________________________
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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