Open lizhuzh opened 4 months ago
PLUMED is not designed for that regime, but rather for the regime where there are a few (10-100) CVs. In addition to startup, I suspect you can have significant overhead also during the simulation if you use 10^4 CVs.
There are a number of CVs that are designed to compute simpler CVs on multiple combinations of atoms (e.g., all pairwise distances in a single CV). If you are more specific about what you are trying to do we can help you to obtain the same result using less CVs
PLUMED is not designed for that regime, but rather for the regime where there are a few (10-100) CVs. In addition to startup, I suspect you can have significant overhead also during the simulation if you use 10^4 CVs.
There are a number of CVs that are designed to compute simpler CVs on multiple combinations of atoms (e.g., all pairwise distances in a single CV). If you are more specific about what you are trying to do we can help you to obtain the same result using less CVs
Thanks for your reply. I indeed want to calculate all pairwise distance between two groups. Which CV do you think can calculate these quantities?
What do you want to do with those distances? There are many variables that combine multiple pairwise distances in different manners, e.g.:
and possibly others
What do you want to do with those distances? There are many variables that combine multiple pairwise distances in different manners, e.g.:
COORDINATION
COORDINATIONNUMBER
CONTACTMAP
DISTANCES
and possibly others
Sorry for the late reply --- I was looking at the manual and the source codes of these CVs. What I want to do is to pass all pairwise distances to another CV (e.g. RESTRAINTS). It seems that I do not have access to these components in the above CVs. Also, it seems that those CVs you mentioned are not parallelized, except COORDINATION.Am I correct?
Are all the restraints identical? If so you can easily do this with COORDINATION
and a switching function, with a lot of flexibility on the form of the restraint (though identical on all distances)
If not you might use CONTACTMAP, with a limited for for the restraint, but different reference distances. And I think it's parallelized.
DRMSD might also be a good option, but I don't know if it's parallelized
Hi PLUMED developers,
I am using GROMACS 2018. In my simulation, I need to calculate large amount (~10^4) of CVs. However, I found that it takes ~30 mins to initialize these CVs at the beginning of simulation. I am wondering why this is the case and whether there is any way to make it faster.
Thanks, Lizhu