Dear Dr. Thomas:
Thank you for your reply. Should I optimize scalpha and scbeta
or other parameters to make dvdl at lambda 0.01 and 0.99 close to 0?
Will the paper reviewer accept a curve with a steep slope at two end?
I am looking forward your reply.
Best Regards!
Denis
2012/8/9 <steinbrt.rci.rutgers.edu>:
> Hi,
>
> check e.g.
>
> Title: Soft-Core Potentials in Thermodynamic Integration: Comparing One-
> and Two-Step Transformations
> Author(s): Steinbrecher, Thomas; Joung, InSuk; Case, David A.
> Source: JOURNAL OF COMPUTATIONAL CHEMISTRY Volume: 32 Issue: 15
> Pages: 3253-3263 DOI: 10.1002/jcc.21909 Published: NOV 30 2011
>
> for the effect of scbeta. The default value should be ok for most
> situations, but is certainly one variable you could optimize. There is no
> correct or incorrect value for scalpha and scbeta, but they influence the
> efficiency of your sampling in a case-dependent manner.
>
> Thomas
>
> On Thu, August 9, 2012 9:37 am, Liu Denis wrote:
>> Dear Dr. Thomas：
>> If I want to use one-step soft core, should I explicitly set the
>> scbeta parameter in input file?
>> I did not set it explicitly because there is a default value in Amber
>> Manual. May it be the reason that I got a strange curve?
>>
>> Best Regards!
>> Denis
>>
>> 2012/8/9 <steinbrt.rci.rutgers.edu>:
>>> Hi,
>>>
>>>> the dvdl curve near lambda 0 or 1 seems to be rather steep, far from
>>>> linear. Is it normal?
>>>
>>> that looks unexpected to me. The appearing/disappearing vdW potential is
>>> quite flat close to the endpoints, so it should by definition not give
>>> large dvdl values. It is hard to say without knowing your system and
>>> setup. Do you have vdW-radii changing that are not in the softcore mask?
>>> Or big changes in solvated charges? Your curve may be perfectly fine,
>>> but
>>> a closer look at what goes on in your system seems warranted...
>>>
>>> Thomas
>>>
>>>>
>>>> What reason may cause such result?
>>>>
>>>> Best Regards!
>>>> Denis
>>>> 2012/7/26 <steinbrt.rci.rutgers.edu>
>>>>>
>>>>> Hi,
>>>>>
>>>>> > The post http://archive.ambermd.org/201002/0108.html </>said
>>>>> softcore
>>>>> > cannot use at lambda <0.01 or >0.99,
>>>>> > Does it support now?
>>>>>
>>>>> no, that limitation has not changed. There is some work in progress to
>>>>> make a new version of TI that would allow l=0/1, but it is not
>>>>> finished
>>>>> yet. However, I have never seen this as really problematic. The dvdl
>>>>> curve
>>>>> should be linear at both ends and you really want the integral over
>>>>> it,
>>>>> so
>>>>> using 0.01 or 0.00 as a fixed-point for numerical integration amounts
>>>>> to
>>>>> the same thing. Unless you want more than a hundred lambda-windows,
>>>>> there
>>>>> is no real gain from simulating in the <0.01 / >0.99 region.
>>>>>
>>>>> > If I want to get the point at Lambda=0, do I have to use "hardcore"?
>>>>>
>>>>> if you really want this point, then yes, you can not use soft core
>>>>> potentials.
>>>>>
>>>>> > Can I mix the result using hardcore at 0 or 1 and using softcore at
>>>>> other
>>>>> > lambda? In other words, at lambda=0 or 1, does softcore and
>>>>> hardcore
>>>>> give
>>>>> > out the same result theoretically?
>>>>>
>>>>> No! Far from it actually, the two approaches amount to very different
>>>>> potential functions and should not even be close in terms of curve
>>>>> shape.
>>>>>
>>>>> Kind Regards,
>>>>>
>>>>> Thomas
>>>>>
>>>>> Dr. Thomas Steinbrecher
>>>>> formerly at the
>>>>> BioMaps Institute
>>>>> Rutgers University
>>>>> 610 Taylor Rd.
>>>>> Piscataway, NJ 08854
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>>
>>>>
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>>>
>>> Dr. Thomas Steinbrecher
>>> formerly at the
>>> BioMaps Institute
>>> Rutgers University
>>> 610 Taylor Rd.
>>> Piscataway, NJ 08854
>>>
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>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Sat Aug 11 2012 - 10:00:04 PDT
