Dear all,
I performed a series of simulations with a potential that is a mixture of pure MM and QM/MM (i.e. of the type V(¦Ë)= (1-¦Ë)*V_MM + ¦Ë*V_QM/MM ) using sander, where ¦Ë is an adjustable parameter used in standard free-energy perturbations in AMBER (¦Ë=0.005,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,0.995 respectively in my simulations).
The initial state is a pure MM state of a formaldehyde molecule solvated by the TIP3P waters, and the end state is a QM state of a formaldehyde molecule solvated by the same TIP3P waters. In other words, both states are described by the same prmtop and inpcrd files. Only the both mdin files have the difference.
The softcore potential is used to transform the pure MM state of the formaldehyde molecule to the QM state.
However, the lamda=0.005 simulation is not carried on. The mdout file gives that
"SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
QM region + cutoff larger than box
cannot continue, need larger box".
I solvate the formaldehyde molecule with a 15 angstroms TIP3P box and set up cutoff=8,
so I visualize the structure of solute and find that the distance between the carbon atom and the oxygen atom reaches about 18 angstroms.
Could you tell me what this happened?
Best Regards,
Pengfei Li
Email:lipengfei_mail.126.com
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Received on Thu Mar 10 2016 - 23:30:03 PST
