Dear Giulia,
To use amber+plumed you don't have to call plumed with a flag, but you just
have to insert the following lines
plumedfile = 'PLUMED_FILE_NAME', plumed = 1,
into your mdin file.
Also, unfortunately, PLUMED is not well tested with Amber, if you go to the
plumed mailing list you can find reports of different misbehaviors.
Restarts are poorly supported, and particularly you can't call the MPI
version of PLUMED with more cores than the ones you are using for AMBER (if
you are running on GPUs, as you shold with Amber, usually 1 to 4...). Also
the CPU and GPU have to communicate constantly at every step with PLUMED,
highly impacting the performance of your simulations with AMBER.
You can run some calculation in PLUMED with it's openMP implementation, but
there aren't many calculations that can be run with openMP unfortunately.
I'm a great supporter of AMBER, I hate every time I have to switch to
GROMACS or LAMMPS, but having said that, I strongly suggest you to use
GROMACS with PLUMED, as it's well tested and you can easily optimize it's
performances with plumed.
PS: that's is true if you have to perform some calculations that are only
available in plumed (METAD, OPES for example) or if you have to use some
CVs that are implemented only in plumed. Otherwise you can easily stick to
AMBER and use the facilities it offers, which usually run much faster. For
example umbrella sampling is easy to perform within AMBER.
Have a nice day,
Domenico
*Domenico Marson*, Ph.D.
Ricercatore T.D. (A) | Research Fellow
Università degli Studi di Trieste | University of Trieste
Department of Engineering and Architecture (DEA)
Molecular Biology and Nanotechnology Laboratory @ UniTS (MolBNL.UniTs)
Via Valerio, 10 - 34127 Trieste (Italy)
domenico.marson.dia.units.it
+39 040 5583437
Skype: domenicomars
On Tue, Jul 19, 2022 at 11:35 AM Giulia Sormani via AMBER <amber.ambermd.org>
wrote:
> Hello to everyone,
>
> I would like to use Amber patched with plumed for some umbrella sampling.
> On the cluster on which I am running (m100 of cineca) there should be
> installed amber2020 patched with plumed2.8.0.
> However, I can t find which is the command to include the plumed.dat file
> in the running, if I run
>
> pmemd.cuda -O -i NVT.in -o umbrella.out -p topology.prmtop -c
> previous.restart -r next.restart -x umbrella.nc -inf umbrella.info -plumed
> plumed.dat
>
> I get the error
> unknown flag: -plumed
>
> Also, on the amber or plumed manuals I can't find info or examples on how
> to do this.
>
> Hope someone can help,
>
> Giulia
>
>
>
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>
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Received on Thu Aug 04 2022 - 13:34:45 PDT
