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

[LuLanyuan]

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
> To: gmx-users at gromacs.org
> 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
>> _________________________________________________________________
>=20
>=20
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