[gmx-users] (no subject)

Christopher Neale chris.neale at alum.utoronto.ca
Sat Apr 18 16:22:19 CEST 2015

Dear Bahare:

this is not necessarily a problem. If what you are saying is that in two separate runs of the same system from the same coordinates you got different trajectories then this is expected under most conditions: http://www.gromacs.org/Documentation/Terminology/Reproducibility

However, if you are saying that your trajectory does not produce a linear increase in output timepoints and has some overlap, then I am a bit surprised since you say that you use the -append option to mdrun. I suspect that this is not your concern, but if it is then please provide more details. It's kind of hard to know since you did not provide your actual complete commands (cut and paste is always best for a list like this; e.g. was it also "-deffnm newmd" in the first run ? if it was actually "-deffnm md" in the first run then what you got is expected behaviour).


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Bahare Meftahi <meftahibahare at yahoo.com>
Sent: 18 April 2015 08:06
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] (no subject)

Thanks chris for your answer. I'm using Gromacs 4.6.3 with AMBER03 force field. i had a 20ns run with this command:mdrun -s    .tpr -v -deffnm  but after some days and passing less than 4 ns of run, power turned out and the run was crashed. i used this command to restart the run:mdrun -s   .tpr -v -deffnm newmd -cpi   .cpt -appendafter finnishing all 20ns of run i calculated RMSD and H-bonds and i noticed that there are times at the bigining of  second part which are common with the end times of first part, but the results of RMSD and H-bonds in these times does not match.I have had the same experience using Gromacs 4.6.7
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