VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Dec 03 2013 - 10:08:48 CST

Hi Shyno,

I've seen this before when I used ParseFEP on simulations that were
conducted independently (each change in lambda corresponding to its own
NAMD run, since otherwise it wouldn't get through the queue). ParseFEP
is very picky about the formatting of the fepout files, especially in
VMD 1.9, and if each NAMD run is done independently, it doesn't write
out some of the pieces ParseFEP expects. What I've done is run very
short simulations (basically the FEP tutorial) where the entire forward
and backward direction were each one NAMD run to see what the output
format is, and make sure that I repeat that format when concatenating my
independent FEPout files together.

Good luck!
-Josh Vermaas

On 12/02/2013 11:42 AM, Shyno Mathew wrote:
> Dear all,
> I am trying to use the parseFEP plugin of VMD version 1.9. FEP
> calculations were done using namd 2.8
> The temperature is set to 300 K, the BAR estimator and disp options
> are turned on. For Gram-Charlier oder, I put 0.
> I am getting the following errors:
> domain error: argument not in valid range
> domain error: argument not in valid range
> while executing
> "expr sqrt($instant_error_gauss) "
> (procedure "::ParseFEP::FEP_formula" line 361)
> invoked from within
> "::ParseFEP::FEP_formula $file $file_entropy $file_lambda $window
> $mean_xi $fororback"
> (procedure "::ParseFEP::normal_parse_log" line 60)
> invoked from within
> "::ParseFEP::normal_parse_log $::ParseFEP::fepofile forward "
> (procedure "::ParseFEP::namdparse" line 172)
> invoked from within
> "::ParseFEP::namdparse"
> (in namespace inscope "::ParseFEP" script line 21)
> invoked from within
> "::namespace inscope ::ParseFEP {
> ##if {$::ParseFEP::fepbofile != ""} {set ::ParseFEP::sosindex 1 }
>
> if { [string length $fepofile] < 1 } {
> tk_dial..."
> invoked from within
> ".parseFEP.runbutton invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .parseFEP.runbutton"
> (command bound to event)
>
> thanks,
> Shyno
>
>
>
> --
> Shyno Mathew
> PhD student
> Department of Chemical Engineering
> Columbia University