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

From: Liu Denis <cndenis.gmail.com>
Date: Sun, 12 Aug 2012 23:01:33 +0800

Dear Prof. case:
     Thank you for your reply!
     Is the vdW-radii and solvated charges defined in prmtop file? If
so, there should not be change outside the scmask. In fact, I did a
null transform, namely use the identical prmtop and inpcrd file for
both V0 and V1, steep slope was still seen at the two end of the
curve.
    I attached my prmtop, input, part of output file at lambda=0.01
after 1ns production run of the null transform in the email. Could you
help me to find out what
is wrong in it?
  Thank you.

0.01 37.10
0.05 13.47
0.10 -1.23
0.15 -7.53
0.20 -11.12
0.25 -12.42
0.30 -12.45
0.35 -10.70
0.40 -8.23
0.45 -4.52
0.50 0.00
0.55 4.66
0.60 8.41
0.65 10.70
0.70 12.05
0.75 12.37
0.80 11.11
0.85 7.79
0.90 0.80
0.95 -13.16
0.99 -37.61

Best Regards!
                  Denis


2012/8/12 Liu Denis <cndenis.gmail.com>:
> Dear Prof. case:
> Thank you for your reply!
> Is the vdW-radii and solvated charges defined in prmtop file? If
> so, there should not be change outside the scmask. In fact, I did a
> null transform e.g. use the identical prmtop and inpcrd file as both
> V0 and V1, steep slope was also seen in the two end of the curve.
> I attached my prmtop, input, output file after 1ns production run
> of the null transform in the email. Could you help me to find out what
> is wrong in it?
>
> 0.01 37.10
> 0.05 13.47
> 0.10 -1.23
> 0.15 -7.53
> 0.20 -11.12
> 0.25 -12.42
> 0.30 -12.45
> 0.35 -10.70
> 0.40 -8.23
> 0.45 -4.52
> 0.50 0.00
> 0.55 4.66
> 0.60 8.41
> 0.65 10.70
> 0.70 12.05
> 0.75 12.37
> 0.80 11.11
> 0.85 7.79
> 0.90 0.80
> 0.95 -13.16
> 0.99 -37.61
>
> Best Regards!
> Denis
>
>
>
> 2012/8/12 case <case.biomaps.rutgers.edu>:
>> On Sun, Aug 12, 2012, Liu Denis wrote:
>>
>>> 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?
>>
>> Let me just reiterate what Dr. Steinbrecher has already said: the default
>> values ought to work well, and the curves you report look quite unusual. You
>> should check the issues brought up in the earlier reply:
>>
>>> 2012/8/9 <steinbrt.rci.rutgers.edu>:
>>
>>> >>>> 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...
>>
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>
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Received on Sun Aug 12 2012 - 08:30:03 PDT
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