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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
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We need the ability to specify weights as an available weight array or list of arrays in TICA + LaggedCovariance. I thought we had decided to do that but it now seems that it's only possible to have c…
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Hello,
I try to use tica with a metadynamics trajectory. Each frame of the trajectory has a different weight which are already precomputed. My problem is, that I do not understand how to use the we…
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read_restart() methods contain mostly duplicated and boilerplate code. Use a parent class implementation and perhaps helper functions to make them shorter and cleaner.
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It has been requested on the questionnaire.
As a side note, it is already possible to implement it by writing properly an input file. Indeed, as far as I understand, funnel metadynamics is just a res…
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It is becoming increasingly difficult (e.g. in message-passing parallelism) to perform an easy bookkeeping of the forces applied to each atom via different code paths (individual atoms vs. scalable gr…
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Hello imp users and developers !
is their anyway that i can generate the form factor file from SAX data and pdb file using imp to use in plumed-gromacs calculations ?.
Previously Dr.Magnus An…
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Hi,
I run path cv using plumed 2.2 with gromacs 5.1.2. But I always get the Segmentation fault. I patch the gromacs code with -p --shared opitions.
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Reading file md.tpr, VERSION 5.1.2 (single pre…
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Hello list:
Could I request the addition of the Steinhardt bond order parameters (Q,W) as a colvars component? These are implemented in the CP2K code, but I was unable to find an implementation here. …
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Hi,
I am running metadynamics with plumed version 1.3.0, ACEMD MD engine package and Amber ff (ff99SB).
I have two CVs with walls on both on them.
1st CV is distance and 2nd CV is torsion.
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DIST…