Nevermind the last question. I was thinking about something completely
different. I guess that the value that really matters is the average for
the simulation. Right?
Fabrício
2013/10/30 Fabrício Bracht <fabracht1.gmail.com>
> Ok. Thanks. Now it says that I have to specify a window size. I guess that
> the answer to this question may vary from system to system, but, is there a
> "consensual" window size?
>
>
> 2013/10/30 Daniel Roe <daniel.r.roe.gmail.com>
>
>> Hi,
>>
>> On Wed, Oct 30, 2013 at 2:02 PM, Fabrício Bracht <fabracht1.gmail.com>
>> wrote:
>> > I have one more question about lifetime analysis. I've tried
>> > hbond bond1 out nhb1.dat :1-342 dist 3 series donormask
>> > :204&!.CA,CB,C|:342.O acceptormask :204.OD1,OD2|:342.O avgout
>> avghb1.dat
>> > solventdonor :WAT.O solventacceptor :WAT.O bridgeout bridge1.dat
>> solvout
>> > solvent1.dat
>> > lifetime lifeout bond1
>> > But I get
>> > Error: lifetime: No data sets selected.
>> > Error: Could not setup analysis [lifetime]
>>
>> This is actually related to how the 'hbond' action generates
>> time-series data. In most actions you know what data you will generate
>> beforehand; for example, with 'distance' you know you will have 1 data
>> set generated containing distances. This data set is created as soon
>> as cpptraj processes the 'distance' command, so any subsequent
>> actions/analyses know that it's there. With 'hbond series' however,
>> cpptraj doesn't know whether any hydrogen bonds will be formed or not,
>> so those data sets aren't created until you actually process your
>> trajectory frames. Therefore the [solutehb] and [solventhb] time
>> series data sets aren't created until you 'run'. The solution is to
>> add a 'run' command after hbond so that trajectory frames are
>> processed and hbond time series data is created, then run the lifetime
>> analysis by itself. For example, something like:
>>
>> hbond bond1 ...
>> run
>> runanalysis lifetime out solute.lifetime.dat bond1[solutehb]
>>
>> Hope this helps,
>>
>> -Dan
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
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>
>
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Received on Wed Oct 30 2013 - 14:00:02 PDT
