Hello,
I am running simulations with AMBER using CHARMM ff. The first simulation
goes well, but when I restart it, the structure looks abnormal with
extraordinarily long bonds and no water box. And here is what I see in my
output file;
NSTEP = 50000 TIME(PS) = 20050.000 TEMP(K) =********* PRESS =
34350.4
Etot = ************** EKtot = ************** EPtot =
**************
BOND = ************** ANGLE = 5189014.5700 DIHED =
22972.7066
UB = 595873504.0402 IMP = 52996.1654 CMAP =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0124 VDWAALS =
**************
EELEC = 44780.3240 EHBOND = 0.0000 RESTRAINT =
-0.0000
EAMBER (non-restraint) = **************
EKCMT = -0.0000 VIRIAL = -1317974.0864 VOLUME =
1777042.3249
Density =
1.0812
and finally I got the following message
ERROR: Calculation halted. Periodic box dimensions have changed too much
from their initial values.
Your system density has likely changed by a large amount, probably from
starting the simulation from a structure a long way from equilibrium.
[Although this error can also occur if the simulation has blown up for
some reason]
The GPU code does not automatically reorganize grid cells and thus you
will need to restart the calculation from the previous restart file.
This will generate new grid cells and allow the calculation to continue.
It may be necessary to repeat this restarting multiple times if your
system
is a long way from an equilibrated density.
Alternatively you can run with the CPU code until the density has
converged
and then switch back to the GPU code.
Here is my command line for restarting simulations
pmemd.cuda -i config.in -p myfile -c restrt.1 -suffix 2
Please let me know if anybody else has seen such an error. I appreciate it.
Thanks,
Sadegh
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Received on Sat Mar 25 2017 - 21:00:02 PDT
