[gmx-users] Re: deshuf.ndx doesn't work for forces?
lulanyuan at msn.com
Fri Jan 25 00:01:19 CET 2008
I think you need to add -force option.
Like trjconv -f a.trr -force -o b.trr
> Date: Thu, 24 Jan 2008 17:39:45 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: deshuf.ndx doesn't work for forces?
> 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.
>> --- Original Message ---
>> I think after the "trjconv -f *.trr -n deshuf.ndx" operation, the new
>> 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
>> use for grompp command. If the output
>> of trjconv is gro/pdb, you're right that it's only deshuffled, but not
>> 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?
>> />>/ 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
>> />>/ 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.
>> />/ As I understand it, the deshuf.ndx file does not allow you to
>> desort, =20
>> />/ merely to deshuffle.
>> />>/ 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?
>> />/ 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, =20
>> />/ 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 =20
>> />/ 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 =20
>> />/ but not -sort.
>> />>/ Thanks a lot.
>> />>/ Lanyuan Lu/
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Windows Live Photo gallery 数码相机的超级伴侣，轻松管理和编辑照片，还能制作全景美图！
More information about the gromacs.org_gmx-users