CHARMM Development Project Forums User Discussion & Questions Molecular Dynamics cnt command in MD simulation input

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

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