Thanks, Ross, for fixing the bug.
I have been just renaming the gamd.log file once a job is done (very likely for many other users too), and didn’t come across this issue. It certainly helps to get this fixed …
Best,
Yinglong
> On Sep 12, 2017, at 11:15 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> Hi Giovanni,
>
> This looks like two bugs. The first is the documentation incorrectly stating -gamdlog instead of -gamd and the second is an actual bug in the code with how the command line is handled when GaMD is active. Thanks to Irfan Alibay for spotting this. We'll get a bugfix added as an update on the AMBER website to fix this.
>
> In the meantime you can try editing the following:
>
> src/pmemd/src/get_cmdline.F90 (around line 270)
>
> call getarg_wrap(iarg, amdlog_name)
> amdlog_specified = .true.
> else if (arg .eq. '-gamd') then
> call getarg_wrap(iarg, gamdlog_name)
> gamdlog_specified = .true.
> else if (arg .eq. '-scaledMD') then
> iarg = iarg + 1
> call getarg_wrap(iarg, scaledMDlog_name)
>
> becomes
>
> call getarg_wrap(iarg, amdlog_name)
> amdlog_specified = .true.
> else if (arg .eq. '-gamd') then
> iarg = iarg + 1
> call getarg_wrap(iarg, gamdlog_name)
> gamdlog_specified = .true.
> else if (arg .eq. '-scaledMD') then
> iarg = iarg + 1
> call getarg_wrap(iarg, scaledMDlog_name)
>
> Then recompile.
>
> All the best
> Ross
>
>
>> On Sep 11, 2017, at 5:37 AM, Battocchio, Giovanni <g.battocchio.tu-berlin.de <mailto:g.battocchio.tu-berlin.de>> wrote:
>>
>> 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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>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Sep 12 2017 - 11:30:03 PDT
