Hi all,
I am simulating a nano-tube using GROMACS. After NVT or NPT level some bonds are removed in VMD. What is the reason? Also, I got the structure using gmx trjconve, but the bonds are still hidden.
Thanks, in advance, for your answers.
Dear Aashish Bhatt
I use gro file. I also used trajectory file and the same was happened.
Macromolecular display programs usually do not use an explicit bond description to draw the bonds, but use a distance cut-off to draw a bond between any two atoms that get closer to each other than that cut-off, up to the number of valencies for that atom, while not drawing any bond between atoms that are farther apart, independent of the theoretical covalent structure of the molecule. Many programs allow you to adjust the default distance cut-off.
For an example, see https://gromacs.org-gmx-users.maillist.sys.kth.narkive.com/RsHir0Wc/gmx-users-bonds-missing-in-vmd-visualization
"VMD computes distances between pairs of atoms to "draw" a bond. So I think your atoms are too distanced from each other. Check the bond distribution during MD and compare with your topology. C-CL should be around 1.76A. VMD will not show this bond if, in the REFERENCE frame (the .gro/pdb you open before the .xtc/.trr), this distance is greater than 2.0A."
"Solutions ! 1) Use "dynamic bonds representation" and set the cut-off to 1.81 or more 2) Find where VMD sets it's standard cutoff for bonds and set it to 1.81 or more forever. 3) VMD FAQ solution is to make a .PSF (topology) to solve this problem. ( You will only need the bond list ) http://www.ks.uiuc.edu/Research/vmd/allversions/vmd_faq.html"
It is possible that the bonds you are observing in your initial structure are not maintained during the simulation due to the use of constraints or constraints algorithms, such as LINCS or SHAKE. These algorithms are commonly used in molecular dynamics simulations to maintain the stability and accuracy of the simulation.
When constraints are applied to the system, VMD may not show the bonds that are constrained, as they are no longer considered dynamic. Therefore, the absence of some bonds in VMD after NVT or NPT simulation may be due to constraints in your system.
Regarding the issue with the bonds still being hidden after using gmx trjconv, it is possible that the output file format does not contain the necessary information to show the bonds. You can try to generate a PDB file format from the output of gmx trjconv, which will contain information about the bonds and should be visible in VMD.
Alternatively, you can try adjusting the bond representation settings in VMD to show all bonds, including those that are constrained or hidden by default.
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