[gmx-users] Re: Re: problems with some calculated trajectories

[Tsjerk Wassenaar]

Hi Bernhard,

The images, are they taken from exactly the same angle? If so, there's
some change in orientation that is just impossible in such a short
time. You didn't happen to fit your structure to a reference prior to
removal of jumps, did you? Fitting messes up PBC and garbles results
from -pbc nojump. If these are not from the original trajectory (mdrun
output), have a look what happens there. Otherwise, trace back all
your steps. Maybe paste here what you've done exactly...

Cheers,

Tsjerk

On Thu, Jun 25, 2009 at 10:10 AM, Bernhard
Knapp<bernhard.knapp at meduniwien.ac.at> wrote:
> 1) trjconv with the "-pbc nojump" option does not help - it removes most of
> the jumps but one big remains- the rmsd for the trajectory is
> http://www.meduniwien.ac.at/msi/biosim/bk/4.jpg
> before the converting with -pbc and
> http://www.meduniwien.ac.at/msi/biosim/bk/4noJump.jpg
> after conversion.
>
> interestingly under linux vmd could load the trajectories which look like
> that:
> http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg
> and
> http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg
>
> 2) Here an illustration for other trajectories with the same problem:
> http://www.meduniwien.ac.at/msi/biosim/bk/1.jpg
> http://www.meduniwien.ac.at/msi/biosim/bk/2.jpg
> http://www.meduniwien.ac.at/msi/biosim/bk/jumppoint.jpg
>
>
> 3) gmxcheck returns no error, just this:
>
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time    0.000
> # Atoms  167731
> Reading frame   20000 time 60000.000
>
> Item        #frames Timestep (ps)
> Step         20261    3
> Time         20261    3
> Lambda       20261    3
> Coords       20261    3
> Velocities    2027    30
> Forces        2027    30
> Box          20261    3
>
>
> any further ideas what I could do with those trajectories or what I shall do
> to avoid such problems in future (integration step, water shell size, ... ?)
>
> cheers
> Bernhard
>
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 22 Jun 2009 16:37:44 +0200
> From: Erik Marklund <erikm at xray.bmc.uu.se>
> Subject: Re: [gmx-users] problems with some calculated trajectories
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A3F9738.7070103 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi,
>
> Could it be a periodicity issue? Have you tried using trjconv -pbc nojump ?
>
> /Erik
>
> ------------------------------
>
> Message: 2
> Date: Mon, 22 Jun 2009 17:19:43 +0200
> From: Martin H?fling <martin.hoefling at lmu.de>
> Subject: Re: [gmx-users] problems with some calculated trajectories
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <806BD6CF-4903-465F-A2B6-8D0FFA98451D at lmu.de>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Hey Bernhard, here some thoughts of mine:
>
> In principle, vmd should be able to read the trajectories if pdb2gmx
> tells you that the trajectory is ok. If this is not the case, you can
> use gmx_rescue64 to extract the undamaged parts.
>
> Reasons for damaged trajectories, even when gromacs runs through fine...
> ... for me - filesystem issues were causing this. In particular this
> happened for me with NFS shares and on Lustre filesystems. My NFS
> problems got solved with an upgrade of the NFS packages on our
> machines (at least 1 1/2 yrs ago).
>
> Best
> 	Martin
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 22 Jun 2009 18:06:13 +0200
> From: Martin H?fling <martin.hoefling at gmx.de>
> Subject: Re: [gmx-users] problems with some calculated trajectories
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <D1212DF6-6341-45D3-8EF6-F975B68CE374 at gmx.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes
>
>
> Am 22.06.2009 um 17:19 schrieb Martin Höfling:
>
>
>
> Hey Bernhard, here some thoughts of mine:
>
> In principle, vmd should be able to read the trajectories if pdb2gmx
> tells you that the trajectory is ok. If this is not the case, you
> can use gmx_rescue64 to extract the undamaged parts.
>
>
>
> ^
> ^^^^^^^^^^
> = gmxcheck :-)
>
> Best
> 	Martin
>
> ------------------------------
>
> Message: 4
> Date: Mon, 22 Jun 2009 13:29:10 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users]	-bash:
> 	/home_soft/soft_chem/soft_install/gromac/bin/GMXRC.bash:	No such file
> 	or directory
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A3FBF66.4010602 at vt.edu>
> Content-Type: text/plain; charset=GB2312
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623