From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Thu Mar 13 2014 - 11:47:28 CDT
On 13 March 2014 18:32, Hongbo Du <hongbodu_at_uark.edu> wrote:
> Hi, Thomas,
>
> I think you can read out all the coordinates in the cell by command
> loadcoords and use a loop to find out the maximal and minimal coordinates
> in x,y,z direction to determine you cell vector.
>
I am not sure if this is accurate because I simulate a membrane system and
lipid tails stick out of the central box.
> By the way, the TCLforces is slow because it is running on one core. If
> you want to speed up, you may try TCLBC.
>
> I cannot use TCLBC because I measure distances between atoms. TCLBC
measures distances between atoms that are within the same patch only.
> Best wishes,
>
> Hongbo
> _______________________________________
> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
> Norman Geist [norman.geist_at_uni-greifswald.de]
> Sent: Thursday, March 13, 2014 8:34 AM
> To: 'Thomas Evangelidis'
> Cc: Namd Mailing List
> Subject: AW: namd-l: how to get cell vectors in tcl forces script
>
> And no error cause of unknown command? You may not "set output lala" only
> do "output lala" as single line.
>
> Norman Geist.
>
> Von: Thomas Evangelidis [mailto:tevang3_at_gmail.com]
> Gesendet: Donnerstag, 13. März 2014 12:12
> An: Norman Geist
> Cc: Namd Mailing List
> Betreff: Re: namd-l: how to get cell vectors in tcl forces script
>
> Just to update you, I tried to use the "output" command within the tcl
> forces script but no file is written, although namd is running.
>
> On 12 March 2014 16:59, Norman Geist <norman.geist_at_uni-greifswald.de
> <mailto:norman.geist_at_uni-greifswald.de>> wrote:
> You need to try. The "output" command will just write a set of restarts
> with the specified name, so hitting:
>
> output test
>
> should result in the following files being created:
>
> test.coor
> test.vel
> test.xsc
>
> The question is just if the "output" command is available within TclForces.
>
> Norman Geist.
>
> Von: Thomas Evangelidis [mailto:tevang3_at_gmail.com<mailto:tevang3_at_gmail.com
> >]
> Gesendet: Mittwoch, 12. März 2014 15:27
> An: Cosseddu, Salvatore
> Cc: Norman Geist; namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>
> Betreff: Re: namd-l: how to get cell vectors in tcl forces script
>
> Hi Norman & Salvatore,
> I also thought about reading in the .xsc file but that would slow down the
> simulation. Fortunately, the cell vectors do not change drastically - and
> precision is
> unnecessary in my case- therefore lowering too much restartfreq is not
> needed.
> Norman can you give an example of using the output command within a
> jobscript file? I don't understand how you can write restart files more
> frequently than restartfreq does.
> thanks,
> Thomas
>
> On 12 March 2014 16:01, Cosseddu, Salvatore <S.M.Cosseddu_at_warwick.ac.uk
> <mailto:S.M.Cosseddu_at_warwick.ac.uk>> wrote:
>
> Hi Norman,
>
>
>
> This is what I usually do, I set restartfreq conveniently. To be honest I
> don't know either about "output" command within tclforces.
>
>
>
> Best wishes
>
> Salvatore M Cosseddu
>
> ________________________________
> From: Norman Geist <norman.geist_at_uni-greifswald.de<mailto:
> norman.geist_at_uni-greifswald.de>>
> Sent: 12 March 2014 12:54
> To: Cosseddu, Salvatore
>
> Cc: Namd Mailing List
> Subject: AW: namd-l: how to get cell vectors in tcl forces script
>
> Yes, I mean I don't know if the "output" command works from TclForces. He
> need to try, otherwise he would have to set the restartfreq suitable for
> his needs.
>
> Norman Geist.
>
> Von: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> [mailto:
> owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>] Im Auftrag von
> Cosseddu, Salvatore
>
> Gesendet: Mittwoch, 12. März 2014 13:06
> An: Namd Mailing List
> Betreff: RE: namd-l: how to get cell vectors in tcl forces script
>
>
> Dear Norman and Thomas,
>
>
>
> It works also within tclforces. You must be ready to a slight loss of
> performance for the additional I/O work. Anyway the following procedure
> has been tested and have worked fine for me since version 2.8. Hope it will
> help
>
>
>
> ------------------------------------
>
> proc readcell {xscfile} {
>
> if {[catch {open "${xscfile}" r} xsc]} {
> puts stderr "ERROR opening ${xscfile}
> CHECK!!!"
> exit 1
> }
>
> set in [read $xsc]
> set bcell [list [lindex $in 28] [lindex $in 32] [lindex $in 36]]
> print "readcell: read cell, at step [lindex $in 27] was $bcell"
> close $xsc
> return $bcell
> }
>
> -------------------------------------
>
>
>
> simply usage:
>
>
>
> set boxcell [readcell <xsc filename>]
>
>
>
> Best regards
>
> Salvatore M Cosseddu
>
>
>
> ________________________________
> From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> <
> owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> on behalf of
> Norman Geist <norman.geist_at_uni-greifswald.de<mailto:
> norman.geist_at_uni-greifswald.de>>
> Sent: 12 March 2014 07:29
> To: 'Thomas Evangelidis'
> Cc: Namd Mailing List
> Subject: AW: namd-l: how to get cell vectors in tcl forces script
>
> Hi,
>
> I was also searching for such a command, but the only way you are
> currently able to do it, seems to be using the "output" command to write a
> set of restarts and read the box info out of the xsc file. No idea if this
> is also possible within TclForces, but its working from jobscript context--089e01227abc6b5aae04f47fb581--
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