From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Mon Oct 20 2014 - 03:28:51 CDT
I am performing graphene-dna simulation I have chosen following procedure:
1. Minimization, with fixed sheet and constraints ON
2. Heating, rescaling from 0 - 310 k, 0.001
3. Equilibration for 5 ns, NPT
4. Minimization again with same specificication
5. Equilibration for 10 ns, NPT
6. Production for long ns, NVT
After heating in the equilibration step after 2 ns graphene sheet turn up side of the box and dna is at the same position simulating. Afterwords, it comes back to its position and goes back to opposite side, in hole NPT simulation this things happened. Further, in NVT simulation, when I start with restart points same thing happen 2-3 times for 20 ns run.
Than I repeated whole procedure with my fixed off and constants off, during NPT equilibration graphene sheet first rotate on its axis to x,y axis, than after few nanoseonds it started the same behaviour to go to opposite side, this increases the RMSD value every time the sheet goes to opposite side.
Could anyone suggest me:
1. How my sheet move like this and stay to its position
2. Constraints variation effect the system I understood but I am not sure how it is effecting the system.
Thanks in advance
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