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Acellera / htmd

HTMD: Programming Environment for Molecular Discovery
https://software.acellera.com/docs/latest/htmd/index.html
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Multiple replicas metadynamics simulations on ACEMD #322

Closed yiannisgaldadas closed 7 years ago

yiannisgaldadas commented 7 years ago

Dear htmd users,

Has anyone ever tried to perform a replica exchange metadynamic simulation using ACEMD? I am trying to find a tutorial or something regarding the format of the acemd input files but I cannot find anything even though in the manual it says that you can perform replica exchange metadynamics with plumed2. For instance, in Gromacs you generate a .tpr and a plumed.dat file for each replica and using a command like to following

mpirun -np 4 gmx_mpi mdrun -s topol -plumed plumed -multi 4

Gromacs identifies all the .tpr and plumed files in the current directory. So I was wondering what is the equivalent "run" command to do the same in ACEMD. I tried to have separate input file for each replica and then submit all the jobs in different GPUs at the same time but it didn't work.

Best wishes, Yiannis

yiannisgaldadas commented 7 years ago

Does anyone know if I need ACEMD Pro in order to run multiple replicas simulations?

j3mdamas commented 7 years ago

Yes, a ACEMD Basic license only allows running on 1 GPU

j3mdamas commented 7 years ago

So, if you don't have a Pro license, you won't be able to use replica exchange.

j3mdamas commented 7 years ago

Please, for ACEMD only related issues, non-related with HTMD, please post them here: https://github.com/Acellera/acemd_issues/issues

yiannisgaldadas commented 7 years ago

But still, how should the run command look like when you want to perform such a simulation? Should somebody submit N jobs, where N is the number of replicas? Or should it be like mpirun -np 8 acemd input_replica1 input_replica2 ... input_replica_N?

j3mdamas commented 7 years ago

Open a new issue on acemd_issues, and it will be addressed there

yiannisgaldadas commented 7 years ago

Thank you very much and apologies for posting it here!!