Re: NAMD minimisation

From: Jan Saam (jan.saam_at_charite.de)
Date: Thu Nov 27 2003 - 08:15:26 CST

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Hello Wong,

you are not minimizing but running a simulation because you commented
out the minimize command:

#script

#minimize 400

run 20000

Without prior minimization your simulation must crash!

Jan

Am Do, 2003-11-27 um 14.29 schrieb Hua Wong:
> Hello. I have trouble with setting up a minimisation under NAMD.
> Here is the NAMD script I use....
>
> # NAMD configuration file for PROT
>
> # molecular system
> structure PROT.psf
>
> # force field
> paratypecharmm on
> parameters ../par_all22_prot.inp
> exclude scaled1-4
> 1-4scaling 1.0
>
> # approximations
> switching on
> switchdist 8
> cutoff 12
> pairlistdist 13.5
> margin 0
> stepspercycle 20
>
> #integrator
> numsteps 10000
> timestep 1
>
> #output
> outputenergies 1
> outputtiming 100
> binaryoutput no
> imdon yes
> imdfreq 1
> imdport 3111
>
> # molecular system
> coordinates PROT.pdb
>
> #output
> outputname PROT_out
> #dcdfreq 1000
>
> # constraints/Fixed
> fixedAtoms on
> fixedAtomsFile PROT.pdb
> fixedAtomsCol B
>
> #protocol
> temperature 400
> langevin no
>
> rescaleFreq 50
> rescaleTemp 400
>
> #script
>
> #minimize 400
>
> run 20000
>
> and the results I obtain
>
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP TOTAL2 TOTAL3
> TEMPAVG
>
> ENERGY: 0 2685892.8098 -99999999.9999 -99999999.9999
> -99999999.9999 -13233.6249 99999999.9999 0.0000
> 0.0000 -99999999.9999 -99999999.9999 -99999999.9999 -99999999.9999
> -99999999.9999 -99999999.9999
>
> ENERGY: 1 -99999999.9999 -99999999.9999 -99999999.9999
> -99999999.9999 -99999999.9999 -99999999.9999 0.0000
> 0.0000 -99999999.9999 -99999999.9999 -99999999.9999 -99999999.9999
> -99999999.9999 -99999999.9999
>
> ENERGY: 2 -99999999.9999 -99999999.9999 -99999999.9999
> -99999999.9999 -99999999.9999 -99999999.9999 0.0000
> 0.0000 -99999999.9999 -99999999.9999 -99999999.9999 -99999999.9999
> -99999999.9999 -99999999.9999
>
> I am a bit puzzled because someone else made a script that is identical
> and it seems to work.....
>
> Any hint?
>
> Thanks
>
> Wong Hua
>

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