[AMBER] problem in amber

From: Robin Jain <robinjain.chem.gmail.com>
Date: Thu, 9 Jul 2015 13:02:05 +0530

Dear all.
I have simulated my molecule in a cubic box of 20.61 A using periodic
boundary condition. After a 60ns run the last line in restart file show
the cell size 20.95 A. Now i want to do a abinito md using cpmd , for this
i got a pdb from last trajectory and then convert it into .xyz file and
then upload into molden to create a cpmd input which show the cell size
25.04 A,

1. why the cell size difference come in classical md and in abinitio md?
2. If i use 20.95 A cell size, the solvent molecules comes out the box in
molden why, they do not come out in AMBER MD.
3. using 20.95 A cell size molden show very poor periodicity while using
25.04 A, it show good one. Why?
Please help me in this regard.
Thanking You.
Robin Jain
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Received on Thu Jul 09 2015 - 01:00:02 PDT
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