From: Luca Bellucci (bellucci14_at_unisi.it)
Date: Thu Aug 31 2006 - 08:00:49 CDT
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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