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cnt command in MD simulation input
#38142 01/05/21 05:19 AM
Joined: Oct 2019
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vht Offline OP
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Hi all,

I used charmm gui to obtain the production run file and when it was started to run, calculation was terminated normally

CHARMM> ! Please set cnt on the command line like this: $charmm cnt=$cnt -i step7_production.inp -o step7_production_${cnt}.out
CHARMM> if @?cnt .eq. 0 stop ! Error: missing value for cnt
Comparing "0" and "0".
IF test evaluated as true. Performing command
VCLOSE: Closing unit 10 with status "KEEP"
VCLOSE: Closing unit 20 with status "KEEP"
$$$$$$ New timer profile $$$$$
Total time 1.90 Other: 0.00

NORMAL TERMINATION BY NORMAL STOP
MOST SEVERE WARNING WAS AT LEVEL 0

$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 1.90 SECONDS
CPU TIME: 1.90 SECONDS

Production file is attached in here.Few questions that I have are,

What is this cnt?

and how to get rid of this?

I am using c44b1 version of charmm

Thanks
VH

Attached Files
step5_production.txt (2.39 KB, 45 downloads)
SHA1: dd72243cfd642592a2d67c503a91c8f6967f7478
Re: cnt command in MD simulation input
vht #38143 01/05/21 04:09 PM
Joined: Sep 2003
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rmv Online Content
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It's not part of CHARMM per se, but a convention used by the CHARMM-GUI folks for their method of running dynamics. The user is expected to set a script variable named cnt on the command line, as indicated in the comment lines in the output you've posted.

There are alternative methods for creating numbered files for long MD runs in the Script Archive forum; for example, see this post


Rick Venable
computational chemist


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