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

[Bernhard Knapp]

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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