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

[David Mobley]

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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