Dear all,
I am using NAMD in combination with PLUMED for the PATH COLLECTIVE VARIABLE (CV) technique.
As reported in the PLUMED manual, the plumed and the NAMD input files are independent.
This means that the NAMD input file is responsible for the dynamics, while the plumed.dat input file regards the PATH CV calculation.
In the NAMD input file I have specified to start the dynamics from the coordinate file (SYS.crd) that correspond to the first frame in the PATH CV "frame_1.pdb".
Additionally, also the NAMD restart files correspond to frame_1.pdb.
in this way:
-----------------------------------------------------------------------------------------------
plumed on
plumedfile plumed.dat
# Input
paraTypeCharmm off
amber on
parmfile SYS.top
ambercoor SYS.crd
readexclusions on # exclusions are taken from the prmtop made by leap
# Restart Options
extendedSystem SYS.restart.xsc
bincoordinates SYS.restart.coor
binvelocities SYS.restart.vel
restartname SYS_1.restart
------------------------------------------------------------------------------------------------
The calculation gave me the following error:
-------------------------------------------------------------------------------------------------
Info: Entering startup phase 8 with 270244 kB of memory in use.
Info: Finished startup with 270244 kB of memory in use.
MOMENTUM: 0 P: NaNQ NaNQ NaNQ L: NaNQ NaNQ NaNQ
PRESSURE: 0 NaNQ NaNQ NaNQ NaNQ NaNQ NaNQ NaNQ NaNQ NaNQ
GPRESSURE: 0 NaNQ NaNQ NaNQ NaNQ NaNQ NaNQ NaNQ NaNQ NaNQ
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOT
AL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 11431.1567 40331.3583 27552.7734 0.0000 -528411.8450 23056.2657 0.0000 0.0000 NaNQ NaNQ NaNQ NaNQ N
aNQ NaNQ NaNQ NaNQ 1807937.6982 NaNQ NaNQ
OPENING EXTENDED SYSTEM TRAJECTORY FILE
--------------------------------------------------------------------------------------------------
Can someone help me??
Thank you
Giulia
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Received on Sat Oct 01 2011 - 12:00:03 PDT
