Re: Re: Alpha P.M.F. with NAMD 2.8

From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Fri Jun 03 2011 - 07:55:52 CDT

Dear Sir           Thank you for the correction. But, after the correction, I get the same error message as I had mentioned you earlier when I was using NAMD_2.8b1. In the last portion of the  output file it states - colvars:   Initializing a new "alpha" component. colvars:     # componentCoeff = 1 [default] colvars:     # componentExp = 1 [default] colvars:     # period = 0 [default] colvars:     # wrapAround = 0 [default] colvars:     # psfSegID = ASYN colvars:     # hBondCoeff = 0.5 colvars:     # hBondCutoff = 3.3 colvars:     # hBondExpNumer = 6 colvars:     # hBondExpDenom = 8 colvars:     Error: cannot add atoms to a dummy group. colvars:     If this error message is unclear, try recompiling with -DCOLVARS_DEBUG. I could not compile the NAMD as suggested by you earlier as I know not how to compile it.  So, I was waiting for the 2.8 version and hoping that the error will not be shown once I use NAMD_2.8. Regards Prathit ________________________________ From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com> To: Prathit Chatterjee <pc20apr_at_yahoo.co.in> Cc: NAMD Mailing list <namd-l_at_ks.uiuc.edu> Sent: Friday, 3 June 2011 5:46 PM Subject: namd-l: Re: Alpha P.M.F. with NAMD 2.8 Dear Prathit, please insert a space between "alpha" and "{", otherwise "alpha" can't be recognized. Giacomo On Jun 3, 2011 1:21 PM, "Prathit Chatterjee" <pc20apr_at_yahoo.co.in> wrote: > Dear Sir, > >          sorry to disturb you again. The 2.8 Version of NAMD has been out and as suggested by you earlier, I tried again to start my alpha p.m.f. calculation with this new NAMD version. Please have a look of my input file format below - > > > colvarsTrajFrequency    100 > colvarsRestartFrequency 2 > analysis                off > ########################### > colvar { >         ############################################ >         name            helix >         width           0.1                     ##given this value so that it comprises with the lower and upper boundary >         lowerBoundary   0.0 >         upperBoundary   1.0 >         outputValue     on > >         alpha{ >                 residueRange    71-82 >                 psfSegID        ASYN >                 hBondCoeff      0.5 >                 angleRef        88 >                 angleTol        15 >                 hBondCutoff     3.3 >                 hBondExpNumer   6 >                 hBondExpDenom   8 > >         } > } > > ############################################# > # Bias type > > metadynamics { >                 colvars                 helix >                 hillWeight              0.01    #height of each hills in kcal/mol >                 newHillFrequency        100 >                 hillWidth               1.253   #[(square root of 2pi)/2] >                 useGrids                on >                 gridsUpdateFrequency    100 >                 dumpFreeEnergyFile      on >                 writeHillsTrajectory    on >         } > > The error which shows now says that - > > colvars:   # name = helix > colvars:   Error: no valid components were provided for this collective variable. > > But, I have seen from the NAMD user guide that I have provided the variables essential for the pmf calculation. > Please help me in this regard.Any suggestion from other expertise will also be very helpful. > > Thanks and Regards > Prathit Chatterjee > 03.06.2011

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