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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Jan 24 18:28:47 CET 2008

> Message: 2
> Date: Wed, 23 Jan 2008 18:56:22 -0500
> From: LuLanyuan <lulanyuan at msn.com>
> Subject: [gmx-users] deshuf.ndx doesn't work for forces?
> To: <gmx-users at gromacs.org>
> Message-ID: <BAY123-W18C08C464C8EEEA1B0C6B6BC3F0 at phx.gbl>
> 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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