PMF of SMD using CHARMM generated trajectories

From: Rathinavelan, Thenmalarchelvi (thenmcr_at_ku.edu)
Date: Mon Sep 10 2007 - 12:31:56 CDT

Hi NMAD users,
     I have used CHARMM for SMD simulations and want to anaylse the data using NAMD/VMD. I have converted CHARMM gereneated trajectories (10 nos.) into the same format as given in the tutorial (da.dat of 10Ala). The data looks like,
   
    0.0000 50.000000 50.000000 ......... 50.000000 0.000000 .......... 0.000000
    2.0000 54.807920 50.733570 ......... 52.059680 -9.555880 .......... -4.059380
    . . . . . .
    . . . . . .
    . . . . . .
   12024.0 230.291930 224.703520 ......... 224.108310 0.136100 .......... 12.503360

(1st column time; column: 2-11 - extension ; column: 12-21 - force)

  
I used the following script to calcuate the PMF in VMD and got an error message indicating that data is missing:

   % package require multiplot
   % source load-traj.tcl
   % foreach l [array names z] {multiplot $t $z($l)}
   % foreach l [array names f] {multiplot $z($l) $f($l)}
   % set dt 2.0
   % set v 0.015
   % set T 0.6
   % set c {}
   % set i 50
   % while {$i <= 230} {lappend c $i; set i [expr $i + $v * $dt] }
   % source calcwork2.tcl
   % foreach l [array names w] {multiplot $c $w($l)}
 
             reating namespace ::Plot::PlotHandle0
            -set 0
            expected floating-point number but got ""

   Can you please help me to find out could be the problem. Note: The script was working fine with 10Ala data given in the tutorial.

Thanks in advance,
Thenmalar

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