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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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Simulating Zinc #848

Closed shozebhaider closed 5 years ago

shozebhaider commented 5 years ago

I am trying to run a simulation which has two non-bonded zinc ions (ff14SB) that are positioned inside a surface cavity. Not surprisingly they fly away during equilibration.

There are other ways to hold them in place. One of them is described in https://www.mayo.edu/research/labs/computer-aided-molecular-design/projects/zinc-protein-simulations-using-cationic-dummy-atom-cada-approach When I follow this approach I get an error just after initial minimisation: # Launch failure: Kernel [scale_coords] grid [0,1,1] block [256,1,1] Shmem [0] Error [1]

A second approach, which is what I would like to follow is a restrained non-bonded model as described here (http://ambermd.org/tutorials/advanced/tutorial20/rnb.htm). While I can provide a consref pdb file that has the applied restraints, how do I treat constraintscaling for a production run? Is there an example that you can provide that has worked for restraints on zinc, water and histidines.

Many thanks

Shozeb

stefdoerr commented 5 years ago

Is this with ACEMD2 or ACEMD3?

shozebhaider commented 5 years ago

ACEMD2

j3mdamas commented 5 years ago

Hi @shozebhaider,

Can you share the files to reproduce that issue?

Regarding the second approach, I am afraid it is not implemented in HTMD, as we do not have MCPB compatibility as of now.

shozebhaider commented 5 years ago

sent the files to support@acellera

j3mdamas commented 5 years ago

OK, will follow there. Closing.