Re: [AMBER] TI with softcore at lambda=0 or 1?

From: Liu Denis <cndenis.gmail.com>
Date: Thu, 9 Aug 2012 21:37:15 +0800

Dear Dr. Thomas´╝Ü
      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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber



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Received on Thu Aug 09 2012 - 07:00:03 PDT
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