Hi Pengfei,
We have the same name. : )
Pengfei
> On Mar 12, 2016, at 1:36 AM, lipengfei_mail <lipengfei_mail.126.com> wrote:
>
> Yeah, I really dont need to use the softcore potential.
> The carbon atom and oxygen atom are in the formaldehye.
> And I found that the distance between them reached about 18 angstroms.
>
> In my simulations, the box size is 15 angstroms and the QM cutoff is 8 angstroms.
> So, in the above described situation, why did only the lamda=0.005 simulation fail?
>
>
> Pengfei Li
>
>
>
>
> On Fri, Mar 11, 2016, lipengfei_mail wrote:
>
>> 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(λ)=
>> (1-λ)*V_MM + λ*V_QM/MM ) using sander, where λ is an adjustable
>> parameter used in standard free-energy perturbations in AMBER
>> (λ=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.
>
> Why do you need or want a softcore potential? It sounds like you have the
> same atoms in the beginning and ending states. If nothing is "appearing" or
> "disappearing", there should be no need for softcores. What did you set for
> your softcore mask?
>
>> 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.
>
> Not sure what carbon atom and oxygen atom you are referring to: are they both
> in the formaldehye? What is your box size? What is your QM cutoff?
>
> Hard to tell what happened, but the above ideas should give you some ideas for
> debugging.
>
> ...dac
>
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Received on Sat Mar 12 2016 - 05:30:04 PST
