[gmx-users] Re: Re: FEP problem with lambda perturbation 1 to 0.95

[Floris Buelens]

Hi Fabricio,

It's not correct to change your value of alpha, you should use a single value for the whole transformation. The soft core potential is constructed so that the end points at lambda=0 and 1 represent the 'native' states (with no influence from the soft core parameters), and that intermediate values produce a smooth transformation. 
Best,

Floris


________________________________
From: Ragnarok sdf <fabracht1 at gmail.com>
To: gmx-users at gromacs.org
Sent: Monday, 10 August, 2009 20:54:35
Subject: [gmx-users] Re: Re: FEP problem with lambda perturbation 1 to 0.95

I have tried using the soft core correction for values of lambda above
0.5, because i read that the overlaping starts usually at this lambda
value. The problem is that now I values of deltaG where lambda is near
0.5 a little bit off-scale. What I mean is that what used to be a nice
sequencial decrease in values from lambda 0 to lambda 1, now gives me
a crazy value for lambda 0.5 (by crazy I mean 3 times larger) then for
lambda 0.55, 0.6, 0.65 etc, I get values 3 times smaller than what
they used to be. I guess that maybe using soft core correction for
lambda values starting from 0.5 was a little bit to soon. But then for
which lambda values should I start using soft core and how would I
justify my choice?
Thank you
Fabrício Bracht
- Ocultar texto das mensagens anteriores -

> I agree with Carsten. See perhaps the discussion at www.alchemistry.org as
> well.
>
> On Fri, Aug 7, 2009 at 2:35 AM, Carsten Kutzner <ckutzne at gwdg.de> wrote:
>
>> On Aug 6, 2009, at 10:57 PM, Ragnarok sdf wrote:
>>
>>  I am performing FEP do obtain the dimerization of a protein in
>>> membrane. The lambda intervals i am using are 0.05 for each window.
>>> After that I rerun each lambda .trr perturbing the system (plus)0.05
>>> and (minus)0.05 lambda value. Then with g-energy I obtain the deltaG
>>> for each delta lambda.
>>> Well, I have encountered a problem when trying to simulate the last
>>> window (1.0 - 0.95 ). The simulation runs for a while and then dies.
>>> The log file says
>>> Step 2200  Warning: Pressure scaling more than 1%.
>>>
>>>  Hi Fabricio,
>>
>> do you use soft-core? If not, I think you need to, at least for
>> the intervals next to 0 and 1 to avoid singularities (these
>> can result in undefined / NaN forces). See chap. 4.5.1 and
>> 7.3.23 in the manual.
>>
>> Carsten
>>
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