I want to use EMC to perform a simple Monte Carlo simulation of a polymer, which only includes a homopolymer with 100 beads and another type of free particle.
I have completed this modeling, but I encountered issues during simulation. I cannot find more information about Moves in the manual.
Regarding MC simulation, I have these questions:
How are the values of these parameters in ‘moves’ specifically represented as’ ncycles’,’ cycles’, and ‘move’? How do I know which steps in the run process have been moved.
What is the content of ‘accept’ in ‘moves’, and how is it currently determined which conformations are acceptable.
In EMC, can I customize the receive function to simulate sampling to the conformation I need.
I am not quite clear on what you are asking, but I will try to answer according to what I think you ask. First of all, a remark: the Monte Carlo routine represented in EMC are designed to work on linear chains only. This means, that one can only use united atom force fields such as OPLS-UA or TraPPE-UA. Typically, one uses displacement, rebridging, repetition, end bridging and end rotation moves to thermodynamically equilibrate a polymer melt or a semicrystalline system. An example of the latter can be found in
The Monte Carlo literature typical uses vernacular like moves and ncycles. One cycle represents the moving of nmobile sites. This means that about half of the mobile sites are moved in case of displacement moves only, since the acceptance of a displacement move is set to be 50%. Please note that ntotal = nmobile+nfixed, where for a semicrystalline system the crystalline sites are fixed and the amorphous sites are mobile. As an example, if have nmobile = 1000 and you set ncycles = 1000 using displacement moves only, it means that you will perform 1,000,000 moves, of which on average you accept 500,000, thus displacing half a million sites.
The term accept has nothing to do with a move being acceptable, but with a move being accepted. In Monte Carlo, one accepts or rejects a move, where in a move a particle or a group of particles is tried to be moved. The accept field records how many moves were accepted. The acceptance rate of a Monte Carlo move is then determined as the ratio of accepted and total trials of this particular MC move. Information on available moves can be found in ‘Chapter 7: Variable Descriptions’ in section ‘Moves’ of the EMC manual as provided by ${EMC_ROOT}/doc/emc/pdf.
EMC offers a number of sampling tools which can be found in ‘Chapter 6: Sampling Tools’ of the EMC manual. Apart from these sampling tools, users cannot define their own sampling routines, since the sampling tools are an integrated part of the code.