[AMBER] CPPTRAJ: Is it a program that requires a large memory?

From: Catein Catherine <askamber23.hotmail.com>
Date: Mon, 27 Aug 2012 15:06:42 +0800

Dear Experts,
I am using cpptraj to analysis my mdcrd files (a total of 6 G gzipped mdcrd files).
However, the jobs stopped in the middle of the analysis without error message, e.g.. The jobs just stopped like this:
----- [md0.mdcrd.gz] (1-100, 1) ----- 0% 10% 20%
I am using the supercomputer to do the analysis, the administrator said it is because of the large memory required by the cpptraj.
Could you mind to share your experience with me how to solve this problem?
My cpptraj file is as follows:===================================================================================parm all.prmtoptrajin md0.mdcrd.gz........trajin md35.mdcrd.gzautoimage anchor :37-460trajout qsub.netcdf netcdf .C1',CArms first out all_all.rms @C1',CAatomicfluct out all.bfactor byres bfactoratomicfluct out all.nobfactor @C1',CA byresaverage all_average_nobox.pdb pdb noboxmatrix correl @C1',CA out all.corr byreshbond out all_hbond.dat avgout all_hbond.datcluster C1 clusters 3 epsilon 4.0 out all.cnumvtime.dat summary all.avg.summary.dat clusterout all.clustertraj clusterfmt netcdf===================================================================================

My qsub commands is as follows:==========================================PGMSTR="$AMBERHOME/bin/cpptraj -i qsub.cpptraj"==========================================
Many thanks,
Catherine
                                               
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Received on Mon Aug 27 2012 - 00:30:02 PDT
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