[gmx-users] To deshuffle or not to deshuffle, that is a question.

[Yang Ye]

On 9/14/2007 5:35 PM, steletch at jouy.inra.fr wrote:
> Selon Yang Ye <leafyoung at yahoo.com>:
>
>   
>> Deshuffling shall be made before 2), 3) and 4).
>>     
>
> Furthermore, be aware that if you use the 'sort' option, you'll also need to
> desort ...
> IIRC, there is a g_desort program that does all in one (it was published on the
> list some time ago), and should be avaialbe in next gromacs version.
>
> Stéphane
>   
Instead, -shuffle and -sort will all disappear in the next version. I 
encourage Frankie to benchmark the speed-up ratio, especially it is not 
a membrane system. I know that people would not use -sort/shuffle so as 
not to mess things up for some "little" lost in speed. That's just alright.
>> On 9/14/2007 11:36 AM, Frankie Montenegro wrote:
>>     
>>> Hi guys,
>>>
>>> A stupid question: I got myself confused with this
>>> shuffling/deshuffling thing, which I
>>>  shouldn't have been doing with protein in the first place. So this
>>> are my steps, done
>>>  on the same 4 nodes, please tell me whether I was supposed to do any
>>> deshuffling
>>>  of .trr and .gro files, and following which steps:
>>> 1)minimization, supplied output .gro to the next step
>>> 2)equilibration, supplied output .gro to the next step
>>> 3) NVT run, supplied output .gro and .trr to the next step
>>> 4) NPT run
>>>
>>> A simple YES or NO for each step will suffice.
>>>
>>> Thanks,
>>> Frankie
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>       
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>     
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>