Dear AMBER users,
Wish you are fine
I performed a 80 ns MD simulation in 8 stages, using AMBER12, each stage
for 10 ns.
*Description of the simulation:*
I used this md control file for all stages
Production
&cntrl
imin=0,
ntx=5,
irest=1,
nstlim=5000000,
dt=0.002,
ntf=2,
ntc=2,
temp0=310.0,
tempi=310.0,
ntpr=5000,
ntwx=5000,
cut=8.0,
ntb=2,
ntp=1,
ntt=3,
gamma_ln=1.0,
/
*The Error*:
70 ns MD simulation was performed without any problems, but the 8th
stage(at 80 ns) failed due to this error below:
>
> | ERROR: I could not understand line 8358
> 56.2239165************-423.4551515 56.1995897************-423.0909738
>
> *s in the inpcrd file often indicate an overflow of the Fortran format used
> to store coordinates in the inpcrd/restart files. This often happens when
> coordinates are not wrapped into the center cell (when iwrap = 0) and some
> particles diffuse too far away. Try restarting from your last good restart
> file and setting iwrap=1 or using a NetCDF restart file format. See the
> Amber manual for details
> "mol500008.out" 58L, 3283C
> 58,1 Bot
>
> I've checked the mailing list for a similar error, but It was not clear
enough for me.
*The question is:*
Regarding the sentence from the mdout file, "Try restarting from your last
good restart file ", how can I know how good the restart file is? does this
simply mean a restart file from a completed stage?!
Is the solution to this just by setting iwrap=1 and resume the 8th stage
using the restart file from the 7th stage, or I have to repeat all the MD
simulation with setting iwrap=1 ?!
Does just setting iwrap=1 and resuming the simulation with the 8th stage
affect the results of the MD simulation?
I also want to point out that I managing to run the MD simulation till 100
ns.
Thanks in advance!
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Received on Tue Aug 11 2015 - 10:30:03 PDT
