Re:RE: Re: [AMBER] cutoff

From: fancy2012 <>
Date: Sun, 6 Jun 2010 15:50:34 +0800 (CST)

Dear Prof. Walker,
Thanks very much for your detailed explanation! I have understand what you have just delivered! Thanks!
And also thank Bill's explanation!
All the best,

2010-06-06"Ross Walker" <> д
>Hi Fancy,
>This is a significantly more complex question than you realize. To begin
>with when you run periodic boundary calculations in AMBER they use the
>Particle Mesh Ewald method by default. I suggest looking up how this method
>works. Essentially it gives you infinite electrostatics without doing
>infinite work. In this situation the cutoff merely serves to divide up the
>calculation between a direct space part and a reciprocal space part. Hence
>in terms of electrostatics you really do not gain much by adjusting the
>cutoff. You'd don't improve the accuracy by much, you simply need to do more
>direct space calculations, which are expensive, and less FFT calculations
>for the reciprocal part which are cheap.
>The VDW interactions, however, are truncated at the cutoff and there is not
>a logical equivalent to PME for dealing with these. However, VDW
>interactions, due to the 1/r^6 dependence fall off very quickly and are
>typically negligible by 8 angstroms. Hence the reason the cut off is set to
>8 angstroms by default. Setting the cutoff below this value will lead to
>large errors due to truncation of the VDW so you should never set it less
>than 8 angstroms. You can gain a little bit by going to 9 angstroms and
>maybe a tiny bit more by going to 10 angstroms. The difference is likely,
>though, to be negligible.
>Thus simply asking what the cutoff should be based on the system you are
>simulating is largely meaningless. Certainly you cannot make things worse by
>increasing the cutoff, you will always improve things but in smaller and
>smaller increments. Meanwhile your calculation time will increase
>considerably. Thus you really have to make a decision between whether you
>gain more by using an 8 Angstrom cutoff and getting more sampling done than
>using a 10 angstrom cutoff and getting less sampling done. Typically you
>will improve your results more by doing more sampling.
>If, however, you are doing an implicit solvent or gas phase calculation then
>there is no PME and the electrostatics are truncated at the cutoff. In this
>case you should typically not use a cutoff, set cut to larger than your
>system size, in order to avoid artefacts due to truncation of the charge
>I hope this helps,
>All the best
>> -----Original Message-----
>> From: [] On
>> Behalf Of fancy2012
>> Sent: Saturday, June 05, 2010 6:21 AM
>> To: AMBER Mailing List
>> Subject: Re:Re: [AMBER] cutoff
>> Dear Bill,
>> Thanks very much for your explanation! what I study is doing MD
>> simulation of EGFR in complex with an inhibitor, so is cutoff of 8
>> angstrom enough? Or 10 is better? Thanks!
>> All the best,
>> fancy
>> 2010-06-05"Bill Ross" <ross.cgl.ucsf.EDU> д
>> >> When we do MD simulations using amber, does cutoff = 10 angstrom
>> will
>> >> make much difference from 8 angstrom?
>> >
>> >In principle over a long simulation it might. Another aspect is that
>> >box clearance should be > cutoff, so with 10A cut you would need a
>> >bigger box, so the expense increases due to more water as well as
>> >more pair evaluations.
>> >
>> >> When choosing 8 angstrom, the calculation will be much faster than
>> >> 10 angstrom?
>> >
>> >Yes, you can try it and see what the difference is for your system.
>> >
>> >> How should we choose?
>> >
>> >I would read the literature for experiments similar to yours.
>> >Without knowing what you are studying, there is no way to know.
>> >
>> >Bill
>> >
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>> >AMBER mailing list
>> >
>> >
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Received on Sun Jun 06 2010 - 01:00:03 PDT
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