[gmx-users] deshuf.ndx doesn't work for forces?

LuLanyuan lulanyuan at msn.com
Thu Jan 24 21:22:11 CET 2008

I think after the "trjconv -f *.trr -n deshuf.ndx" operation,  the new orders of x and v in the trr file are correct. 
Here "correct" means the order is the same as the intitial *.gro file you use for grompp command. If the output
of trjconv is gro/pdb, you're right that it's only deshuffled, but not desorted. But since there's no force in the gro
file, the bug i mentioned is only in the case when you choose trr as the output of your deshuffle operation.
Lanyuan Lu
> Date: Thu, 24 Jan 2008 12:28:47 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] deshuf.ndx doesn't work for forces?
>> Message: 2
>> Date: Wed, 23 Jan 2008 18:56:22 -0500
>> From: LuLanyuan 
>> Subject: [gmx-users] deshuf.ndx doesn't work for forces?
>> To: 
>> Message-ID: 
>> Content-Type: text/plain; charset="gb2312"
>> Hello All,
>> I found sth like a bug regarding the deshuffle index file. I did a   
>> simulation using multiple cpus and -sort -shuffle options. After   
>> that I tried to use the deshuf.ndx file to recover the original atom  
>>  order for my trr file by trjconv -n deshuf.ndx ... command.
> As I understand it, the deshuf.ndx file does not allow you to desort,  
> merely to deshuffle.
>> But by checking the output trr using the gmxdump, I found the oders  
>> of x  and v were deshuffled while the f oder remained unchanged. In   
>> another word the values of forces were not consistent with those of   
>> positions and velocities in the new trr file.
>> Is this a bug?
> So the order of the positions and velocities has changed, but are they  
> correct? I do not believe that gromacs 3.3.1 is capable of desorting,  
> nor is it supported. I have uploaded a tool called g_desort to the  
> users contribution section. It works well and is tested, but it's  
> usage is complicated when you want to load in .trr files via grompp.
>> And is there anyway to get the correct oder for forces also?
> I suggest that you try to reproduce this problem while using -shuffle  
> but not -sort.
>> Thanks a lot.
>> Lanyuan Lu
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