hello everyone, After doing md simulation with no. of steps 1 ns ,my peptide which is of 7-8 residue move out of the boundary of water box.
tell me what shd i do get rid of this problem. Also i want to know about the wall of the box, whether it is permeable or semi-permiable. this is very silly question. Is there something, from which i can know about the dimension of the box and about the membrane so that i can change it when i have to simulate a peptide Thanks in advance Bhawana
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