I am looking at a range from 0.005 to 0.995, where as in between the two
end values i have chosen a spacing of 0.05
So the to perform mbar analysis I should perform my simulations rather
with the cuda implementation?
On 12/15/2015 04:17 PM, Hannes Loeffler wrote:
> The problem with sander is that it can't sample the end-points but
> rather only points up to 0.005 away (so the range is 0.005 to 0.995).
> This necessarily means that there would be some missing energies and
> thus some error if you only did MBAR analysis over that range. Sander
> could principally estimate the MBAR end-point energies but proper
> BAR/MBAR requires explicit sampling of all lambda points. The latter is
> also a problem because the namelist variables bar_l_* only allow you to
> set up an equally spaced array.
>
> What is the lambda range you are look at?
>
> Overall I don't know if there is a useful scheme to support this type
> of analysis for sander. That's why I have decided to not support it.
>
>
> On Tue, 15 Dec 2015 15:42:18 +0100
> Johannes Loeffler <johannes.r.loeffler.gmail.com> wrote:
>
>> Thank you for your fast answer!
>> I just seem to run into another problem;
>>
>> Note: BAR/MBAR results are not computed.
>>
>> is printed out whenever I try to run the script. I used the sander
>> module of AMBER 14. Might that be a problem?
>>
>> Thanks again Johannes
>>
>> On 12/15/2015 02:46 PM, Hannes Loeffler wrote:
>>> https://github.com/MobleyLab/alchemical-analysis
>>>
>>> or better yet my fork which has a few more bug fixes
>>>
>>> https://github.com/halx/alchemical-analysis
>>>
>>>
>>> On Tue, 15 Dec 2015
>>> 14:36:06 +0100 Johannes Loeffler <johannes.r.loeffler.gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> I am trying to perform mbar analysis and was wondering if there are
>>>> any tutorials on how to extract the output from amber out files. In
>>>> the simulations ifmbar=1 flag was naturally included!
>>>>
>>>> Thanks for your input
>>>>
>>>> Joe
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 15 2015 - 07:30:06 PST
