VMD-L Mailing List

From: R. Charbel Maroun (charbel.maroun_at_inserm.fr)
Date: Mon Feb 13 2012 - 05:58:52 CST

Dear Salvatore,

Thanks for your reply. Indeed, "bincoordinates" is a binary coordinate
restart file generated by an NAMD run, but "coordinates" is a pdb file
not generated by an NAMD run, and NAMD cannot do without that file.
So, in between NAMD runs, I have to convert coor files into pdb files.

By script I meant actually a shell script and a VMD script. For the
first one, I I came up with :

#!/bin/bash
charmrun ++local +p8 /usr/local/NAMD_2.8_Linux-x86_64/namd2
step6.5_equilibration.inp > step65A.log;
vmd -dispdev text -e vmd65A.com;
charmrun ++local +p8 /usr/local/NAMD_2.8_Linux-x86_64/namd2
step6.6_equilibration.inp > step66A.log;
vmd -dispdev text -e vmd66A.com;
charmrun ++local +p8 /usr/local/NAMD_2.8_Linux-x86_64/namd2
step7.1_production.inp > step71A.log;
vmd -dispdev text -e vmd71A.com;

where vmd*.com are the VMD Tcl command files obtained by turning on
the Log Tcl Commands option in VMD so as to be able to read coor and
psf files from a previous run and save as pdb for the next run.

Cheers,

CM

Salvatore Mario Cosseddu <S.M.Cosseddu_at_warwick.ac.uk> a écrit :

> Dear Charbel
>
> This is the command
> vmd -dispdev none
> or
> vmd -dispdev none
>
> for your purpose do you know "bincoordinates"? Have a look in the NAMD guide.
> You don't need a pdb file, NAMD can read its own binary files.
>
> Anyway, what do you mean by script? Bash script? Does something like
> this look fine?
>
> #!/bin/sh
>
> ###############
> #a lot of shell scripting here
> ####################
>
> # VMD call
> echo "animate read coor filename.coord waitfor all ;
> [atomselect top all] writepdb filename.pdb
> " | vmd -dispdev none -eofexit
>
> ###############
> #a lot of more shell scripting here
> ####################
>
> exit 0
>
>
> Be careful to escape " and $
>
> To answer to your second question, look to this option "binaryoutput"
> in the manual. Try if setting it as "no" is what you are looking for.
> But you lose accuracy in case you'd like to restart your simulation.
>
>
>
> On 10/02/12 11:26, R. Charbel Maroun wrote:
>> Hello VMDers,
>>
>> Is it possible to run VMD in stand-alone (non-graphical) mode ?
>> Within a script, I just want to be able to read a .coor NAMD binary
>> file and save it as an ASCII
>> .pdb file for further use in NAMD.
>>
>> An alternative question is, how can I get NAMD to write a .pdb file
>> after an MD ? I tried writepdb <filename> in an NAMD script and it
>> gives the following error:
>>
>> ------------- Processor 7 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: Setting parameter writepdb from script failed!
>>
>> I use VMD 1.9 and NAMD 2.8.
>>
>> Cheers,
>>
>> CM
>>
>>
>>
>> ----------------------------------------------------------------
>> This message was sent using IMP, the Internet Messaging Program.
>>
>>
>
> --
> Salvatore Cosseddu
> PhD student
>
> Centre for Scientific Computing and School of Engineering
> University of Warwick
> Coventry CV4 7AL
> United Kingdom
>
> email: S.M.Cosseddu_at_warwick.ac.uk

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