> On Feb 26, 2016, at 2:34 PM, Gerald Monard <Gerald.Monard.univ-lorraine.fr> wrote:
>
>
>
>> On 02/26/2016 10:52 PM, Adrian Roitberg wrote:
>>
>>
>>> On 2/26/16 4:47 PM, Gerald Monard wrote:
>>> Hi,
>>>
>>> Not against, but as a regular pymol user, I won't be able to load
>>> trajectories without converting back to text format...
>>>
>>> Gerald, who really needs to learn VMD someday...
>>
>> no,no, The proper warning is Gerald, who will learn that netcdf saves
>> tons of time and disk space !
>
> I am not that convinced by the disk space: when I gzip my text file, I
> usually get smaller files that the netcdf ones.
But you still need larger disk before doing the zipping :p. Zipping 100 GB of text file is pain to me.
But FYI: we are developing the protein/dna viewer in Jupyter notebook (to unite most of analysis tools in amber in a single working environment). The viewer uses pytraj/cpptraj for trajectory loading, so guarantee that it can work well with amber ecosystem.
http://amber-md.github.io/pytraj/latest/trajectory_viewer.html
Hai
> However, I do agree that
> they are more convenient to handle and faster to process with cpptraj.
>
> G.
>
>>>
>>>> On 02/26/2016 09:55 PM, Hai Nguyen wrote:
>>>> +100 for setting ioutfm=1. It's really pain to analyze and store text file.
>>>> Users tend to follow what developers suggest or set, so this is big favor
>>>> for them too.
>>>>
>>>> I am neutral about ntxo=2
>>>>
>>>> Hai
>>>>
>>>>> On Friday, February 26, 2016, Ross Walker <ross.rosswalker.co.uk> wrote:
>>>>>
>>>>> Hi All,
>>>>>
>>>>> We still have ioutfm=0 as default in git master for pmemd.
>>>>>
>>>>> Is there any reason we couldn't make ioutfm=1 the default for AMBER 16?
>>>>> This can give some real performance benefits, especially on systems shared
>>>>> filesystems.
>>>>>
>>>>> Secondary question - could we also make ntxo=2 default at the same time?
>>>>> (not as critical now ntwr = nstlim by default).
>>>>>
>>>>> All the best
>>>>> Ross
>>>>>
>>>>> /\
>>>>> \/
>>>>> |\oss Walker
>>>>>
>>>>> ---------------------------------------------------------
>>>>> | Associate Research Professor |
>>>>> | San Diego Supercomputer Center |
>>>>> | Adjunct Associate Professor |
>>>>> | Dept. of Chemistry and Biochemistry |
>>>>> | University of California San Diego |
>>>>> | NVIDIA Fellow |
>>>>> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
>>>>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk <javascript:;> |
>>>>> ---------------------------------------------------------
>>>>>
>>>>> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>>>>> be read every day, and should not be used for urgent or sensitive issues.
>>>>>
>>>>>
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>
> --
> ____________________________________________________________________________
>
> Prof. Gerald MONARD
> SRSMC, Université de Lorraine, CNRS
> Boulevard des Aiguillettes B.P. 70239
> F-54506 Vandoeuvre-les-Nancy, FRANCE
>
> e-mail : Gerald.Monard.univ-lorraine.fr
> tel. : +33 (0)383.684.381
> fax : +33 (0)383.684.371
> web : http://www.monard.info
>
> ____________________________________________________________________________
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Received on Fri Feb 26 2016 - 21:30:03 PST
