VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Oct 02 2007 - 18:55:14 CDT

Oops, also, the frame settings should be frame 0, not frame $i. Please
excuse me while I go find something caffeinated...
Peter

Peter Freddolino wrote:
> Hi Narender,
> for what you're trying to do, you're certainly going to need to write
> different output files for each frame (and then combine them later). I
> realize that the instructions I gave you earlier were incomplete, and
> I'm sorry for the error; the best way (currently) to get what you want
> is really going to be to force namdenergy to write a different first
> frame at each iteration:
>
> package require namdenergy
> set sel1 [atomselect top protein]
> set sel2 [atomselect top "water and same residue as within 4 of protein"]
> for {set i 0} {$i < [molinfo top get numframes]} {incr i} {
> $sel1 frame $i
> $sel2 frame $i
> namdenergy -sel $sel1 $sel2 -elec -skip [molinfo top get numframes]
> -par par_all27_prot_na.prm -extsys x.xsc -pme -ofile elect1-$i.dat
> -switch 10 -cutoff 12
> animate delete end 0
> }
>
> If this still does not work, please send me the output you get with the
> -debug flag set. Again, I'm sorry for the mistake on my part. As I said,
> there will be an easier interface for this in the next release of VMD.
>
> Best,
> Peter
>
> Narender Singh Maan wrote:
>
>> Hello,
>> I am having some problem in running namdenergy.
>> I am doing the text version as:
>> .................................................................................
>> vmd -dispdev text -psf x.psf -pdb x.pdb -dcd x.dcd
>> .................................................................................
>>
>> and my script is:source x.tcl
>> .............................................................................................................................
>>
>> package require namdenergy
>> set sel1 [atomselect top protein]
>> set sel2 [atomselect top "water and same residue as within 4 of protein"]
>> for {set i 0} {$i < [molinfo top get numframes]} {incr i} {
>> $sel1 frame $i
>> $sel2 frame $i
>> namdenergy -sel $sel1 $sel2 -elec -par par_all27_prot_na.prm -extsys
>> x.xsc -pme -ofile elect1 -switch 10 -cutoff 12
>> }
>> ...............................................................................................................................
>>
>>
>> but when its done, i don't see any output file (i gave the option of
>> output file "-ofile elect1").
>> Please let me know what i am missing in the script.
>> Thank you
>> singh
>>