Hi all,
I'm quite new to amber and I have problem with the gamd.log for a Gaussian Accelerated Molecular Dynamic simulation.
I'm running a 500ns production gamd simulation, split in 50 input files of 10ns each.
I managed to obtain different output and trajectory files for each input (prod0.in -> prod0.out, prod0.nc)
But the gamd.log file, automatically generated, is overwritten at the end of each run.
I tried to add the submission flag "-gamd" as suggested by pmemd, like this
-gamd gamd_prod0.log
but I get
unknown flag: gamd_prod0.log
usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -frc mdfrc -e mden -inf mdinfo -l logfile]
[-amd amdlog_name -gamd gamdlog_name -scaledMD scaledMDlog_name -suffix output_files_suffix]
PMEMD Terminated Abnormally!
and if I try this other, as suggested in the Amber16 manual (page 393, "The name of the log file can be set to a user defined name by using the command line option -gamdlog
when running Amber."), like
-gamdlog prod0.log
I get
unknown flag: -gamdlog
usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -frc mdfrc -e mden -inf mdinfo -l logfile]
[-amd amdlog_name -gamd gamdlog_name -scaledMD scaledMDlog_name -suffix output_files_suffix]
PMEMD Terminated Abnormally!
do you have any suggestion?
I googled it, but with very few results.
Thanks!
Giovanni
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Received on Mon Sep 11 2017 - 03:00:02 PDT
