Message: 2
Date: Wed, 23 Jan 2008 18:56:22 -0500
From: LuLanyuan <[EMAIL PROTECTED]>
Subject: [gmx-users] deshuf.ndx doesn't work for forces?
To: <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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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