The periodic boundary conditions for my simulation are wrong at some point, can anyone suggest a way to know the optimal values for these parameters? This image of my molecule seems to create a error in simulation.
Before starting your simulation have the periodic boundary condition.....by using the comand....
Set sel [atomselect top all]
$sel get minmax
it will give you the correct dimensions of the box....
Use wrapall keyword in the namd input file.....
If you just want to see your molecule without the water solvent molecule then just visualize your pdb file with VMD and remove the water molecules from there.
http://www.ks.uiuc.edu/Research/namd/mailing_list/
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/
Open the pdb file, remove all water/Sol molecules and save it...Then open it in a molecular viewer tool.
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