From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Aug 31 2006 - 09:35:57 CDT
Hi Luca,
could you let me know what versions of VMD and NAMD you're using, and
what OS? And can I verify your procedure: You loaded your psf and dcd
into vmd and then ran namdenergy? How many frames did your dcd have? It
looks like there's only one frame of namdenergy output...
Peter
Luca Bellucci wrote:
> Hi all,
> I have dcd file named file.dcd for a MD of this kind:
> NPT PME with these option
> dcdfreq 150
> xstFreq 150
> wrapAll on
> dcdUnitCell yes
> Then I have this script (arranged by NAMDEnergy VMD script) for
> post-analysis:
>
> \ structure file.psf
> \ paraTypeCharmm on
> \ parameters par_all27_prot_lipid_na.inp
> \ numsteps 1
> \ exclude scaled1-4
> \ outputname namd-temp
> \ temperature 0
> \ cutoff 12
> \ switchdist 10
> \ pairInteraction on
> \ pairInteractionGroup1 1
> \ pairInteractionFile namd-temp.pdb
> \ pairInteractionGroup2 2
> \ coordinates namd-temp.pdb
> \ run 0
> \ set ts 0
> \ coorfile open dcd namd-temp.dcd
> \ while { ![coorfile read] } {
> \ firstTimestep 0
> \ run 0
> \ incr ts 1
> \ }
> \ coorfile close
>
> But the output for energy is wrong. For example:
> ELECT VDW
> 1427.4544 99999999.9999
> File namd-temp.dcd generated by
> NAMDEnergy script from my original file.dcd. Is this a problem?
> Have you any solution?
>
> Thanks
> Luca
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