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MAXTimesteps in CORREL
#34122 07/07/14 02:10 PM
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Hi CHARMM users!

Hope you have enjoyed your holiday! I have a question about the "MAXTimesteps" flag in CORREL. The documentation says "The MAXTimesteps value is the largest number of steps any
time series will contain." But I still don't understand whether it corresponds to the number of snapshorts or the MD steps in the trajectory. Say I have a trajectory with 1500000 MD steps. As the printing frequency is 500 MD steps thus I have 3000 snapshorts in total. But I don't know which value should be specified for "MAXTimesteps". I tried both and they gave the same outputs. Hope someone can help. Thanks in advance!

Best


Zhi (Shane) Yue
Department of Chemistry
University of Chicago
Re: MAXTimesteps in CORREL
shane yue #34123 07/07/14 02:30 PM
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An update. Seems that "MAXTimesteps" corresponds to the number of snapshots. If I specified the flag with any number smaller than the number of snapshorts in the trajectory read in, CHARMM died due to the error:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
***** LEVEL -2 WARNING FROM *****
***** TOO MANY TIME STEPS. REMAINDER IGNORED
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

I adapte my script from the one wrote by Lennart Nilsson and updated by Jianhan Chen (http://mmtsb.org/workshops/mmtsb-ctbp_wo...ial.html#orient). That script wrote
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
READ TOP/PAR, PSF/PDB, DCD ...

! by default, let's look at Gly41 (the most flexible residue from nmr
! relaxation analysis; see nmr.inp and plot_nmr-s2.gnu)
if @?rid eq 0 set rid = 41

!Open the output file and write header
open write unit 11 card name phipsi-dist.dat
write title unit 11
*#phi and psi distribution of residue: @rid
*#angle p_phi p_psi
*

open write unit 12 card name phipsi.dat
write title unit 12
*#phi and psi time series of residue: @rid
*#time phi psi
*

!Invoke CORREL mode
correl maxtime ?nfile maxseries 2 maxatoms 10

COMPUT TIME SERIES AND HISTOGRAMS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When I directly copied the command line, the "?nfile" was substituted by 1000 and killed the CHARMM. I do not know where "?nfile" came from and what it referred to. I searched subst.doc but found nothing.

Does anyone have any idea? Thanks again.

Best


Zhi (Shane) Yue
Department of Chemistry
University of Chicago
Re: MAXTimesteps in CORREL
shane yue #34126 07/07/14 04:29 PM
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See subst.doc


Rick Venable
computational chemist

Re: MAXTimesteps in CORREL
rmv #34127 07/07/14 04:58 PM
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Thanks Rick.

I double checked subst.doc. ?nfile is the number of frames in the most recently read trajectory file. That explains my problem. Thanks again.

Best


Zhi (Shane) Yue
Department of Chemistry
University of Chicago

Moderated by  BRBrooks, lennart, rmv 

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