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

[Chris Neale]

My apologies, The commands should have been:

trjconv -f a.trr -o b.trr
gmxdump -f a.trr > a.dump
gmxdump -f b.trr > b.dump
diff a.dump b.dump > ab.diff

Chris Neale wrote:
> OK, I can confirm this for 3.3.1. However, I don't think that the 
> problem is one of shuffling or sorting but simply that
> trjconv -f a.trr -o b.trr creates an exact copy of the .trr file 
> *without* the forces. You can easily verify this by doing this:
>
> trjconv -f a.trr -o b.trr
> gmxdump -f a.trr > a.dumo
> gmxdump -f b.trr > b.trr
> diff a.trr b.trr > ab.diff
>
> Note that b.trr is of smaller size then b.trr and the ab.diff file 
> clearly shows that it is the forces that are missing.
>
> I actually have never tested that before now so it appears that my 
> g_desort routine will lead to the loss of force information at each 
> re-sorting event by nature of passing through trjconv -o .trr.
>
> I did take a quick look at the gmx_trjconv code but I am unable to 
> determine the particular place where the code might be changed.
> However, I think that I have isolated it to the need to add an output 
> of force data from the -o .trr option to trjconv.
>
> Chris
>
>
>
> --- Original Message ---
>
> Hi,
> I think after the "trjconv -f *.trr -n deshuf.ndx" operation,  the new 
> or=
> ders of x and v in the trr file are correct.=20
> 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 
> de=
> sorted. 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 
> <http://www.gromacs.org/mailman/listinfo/gmx-users>
> />/ To: gmx-users at gromacs.org 
> <http://www.gromacs.org/mailman/listinfo/gmx-users>
> />/ Subject: [gmx-users] deshuf.ndx doesn't work for forces?
> />/=20
> />>/ Message: 2
> />>/ Date: Wed, 23 Jan 2008 18:56:22 -0500
> />>/ From: LuLanyuan=20
> />>/ Subject: [gmx-users] deshuf.ndx doesn't work for forces?
> />>/ To:=20
> />>/ Message-ID:=20
> />>/ Content-Type: text/plain; charset=3D"gb2312"
> />>/
> />>/
> />>/ Hello All,
> />>/ I found sth like a bug regarding the deshuffle index file. I did 
> a  =20
> />>/ simulation using multiple cpus and -sort -shuffle options. After  
> =20
> />>/ that I tried to use the deshuf.ndx file to recover the original 
> atom =20
> />>/  order for my trr file by trjconv -n deshuf.ndx ... command.
> />/=20
> />/ As I understand it, the deshuf.ndx file does not allow you to 
> desort, =20
> />/ merely to deshuffle.
> />/=20
> />>/ But by checking the output trr using the gmxdump, I found the 
> oders =20
> />>/ of x  and v were deshuffled while the f oder remained unchanged. 
> In  =20
> />>/ another word the values of forces were not consistent with those 
> of  =20
> />>/ positions and velocities in the new trr file.
> />>/ Is this a bug?
> />/=20
> />/ So the order of the positions and velocities has changed, but are 
> they =
> /=20
>> / correct? I do not believe that gromacs 3.3.1 is capable of 
>> desorting, =20
> />/ nor is it supported. I have uploaded a tool called g_desort to the 
> =20
> />/ users contribution section. It works well and is tested, but it's =20
> />/ usage is complicated when you want to load in .trr files via grompp.
> />/=20
> />>/ And is there anyway to get the correct oder for forces also?
> />/=20
> />/ I suggest that you try to reproduce this problem while using 
> -shuffle =20
> />/ but not -sort.
> />/=20
> />>/ Thanks a lot.
> />>/ Lanyuan Lu/
>
>