I am running simulations of a short peptide in GROMACS 4.6 and I noticed that my peptide stretches out to almost cover the whole diameter of the dodecahedral box. I am wondering if the periodic boundary conditions can cause ends that are far from each other to actually touch across boundaries and thus produce unwanted effects.
See attached photo. The starting conformation was collapsed and this is a snapshot after several hundred nanoseconds.
Thanks!
Yes, this would be a minimum image violation and is artificial. You always need to account for the possibility of extension in cases like this. Your box size needs to be as large as required for a fully extended state.
Yes, this would be a minimum image violation and is artificial. You always need to account for the possibility of extension in cases like this. Your box size needs to be as large as required for a fully extended state.
Is gmx mindist the best way to assess whether such violations are occurring? I saw in other forums that mindist has had some problems in the past..
If you can, please post the following details of your simulation.
Which protein are you working on and what is its hydrodynamic radius? What is the size of the box you've taken? while doing "editconf" what criteria did you set about minimum image convention (MIC)?
It seems that the box is not big enough so a violation of MIC is occurring. MIC ensures that the protein doesn't see its periodic image.
You may try simulating with a larger box.
Thank you, I am working on a 35 amino acid peptide that is known to extend from a collapsed state and since the initial structure was the collapsed stated, I didnt think to account for the extension when choosing the box size. So I most probably need a bigger box.
However, I am just wondering if it possible that if the molecule diffuses to a corner in the box, can the same problem occur even though the box is large enough since the effective size of the box at the corners is smaller? I am using a dodecahedron box.
There is no "corner" of a periodic system. If the box dimensions are large enough to accommodate the extended state of the peptide, there is no minimum image violation as it is not dependent on any relative position of the peptide. gmx mindist -pi is the best way to assess minimum image violations.
There is no boundary in periodic boundary condition...you can't say things like "corner of the box", "near the wall" etc. The box you are seeing is just kind of an illusion.
This things may seem a little confusing, If you haven't read the famous book on simulation of liquids by Allen and Tildesley, read the first chapter section 1.5. You may also consider reading "Understanding Molecular Simulation: From Algorithms to Applications" by Frenkel-Smit.
Hope that will help
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