Re: Minimization is taking a lot of computing time.

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Tue Aug 09 2011 - 12:42:17 CDT

Kartheek

You have bigger system (35064 atoms) than you state. Check your system
in some graphical editor, e.g. VMD, Vega. You have some atoms too close
to each other, so you could fix this manually. Then try first to
minimize only side chain (if only protein is in the system, if you also
have nucleic acids chain, check protonation states also), than minimize
whole system. Also check is some already minimized and equilibrated
system run equally slow on your node if this is a case maybe namd should
be compiled on different way. At the end NAMD 2.8 is better choice than
2.7.

On 8/9/2011 1:06 PM, Kartheek wrote:
> Here i am providing an URL to access output file.
> http://researchweb.iiit.ac.in/~kartheek.p/min.out
> ----- Original Message -----
> From: "Kartheek"<kartheek.p_at_research.iiit.ac.in>
> To: namd-l_at_ks.uiuc.edu
> Sent: Friday, August 5, 2011 3:23:42 PM
> Subject: Minimization is taking a lot of computing time.
>
> Dear NAMD users.
> I am started running a minimization for a system of nearly 16,060 atoms,minimization has been running since 48 hours on an eight processor system. Here is my configuration file.Some one please tell me what is the reason behind such a long minimization process.
> Thanks in advance.
>
> # periodic boundary conditions
>
> cellBasisVector1 122.0 0.0 0.0
> cellBasisVector2 0.0 42.0 0.0
> cellBasisVector3 0.0 0.0 40.0
> cellOrigin 0.1 0.2 0.2
> #extendedSystem md018_rst.xsc
>
> xstfile min.xst
> xstfreq 600 # same as dcd freq
> wrapwater on # off is default
> wrapall off # off is default
>
> # simulation space partitioning
>
> cutoff 10.0
> switching on
> switchdist 8.0
> pairlistdist 12.0
> #pairlistMinProcs 72
> margin 4.0 # 0.0 is the default value
>
> # timestep parameters
>
> #numsteps 7200000
> timestep 1.0 # in femtoseconds
> firsttimestep 0
> stepspercycle 24 # default
>
> # basic dynamics
> exclude scaled1-4
> 1-4scaling 1.0
> temperature 300.0 # initial temperature (K)
> dielectric 1.0 # default
> rigidbonds none # options : none,water,all
> rigidtolerance 1.0e-8
> rigiditerations 100
> usesettle on
>
> # PME parameters
> pme yes # 'on' is also possible
> pmegridsizex 125
> pmegridsizey 45
> pmegridsizez 43
> pmeinterporder 6
>
> # Multiple timestep parameters
> fullelectfrequency 6
> nonbondedfreq 2
> mtsalgorithm impulse
> longsplitting c1
> molly on
> mollytolerance 0.00001
> mollyiterations 100
>
> # input files
> coordinates ionized.pdb # PDB file
> structure ionized.psf # Xplore PSF file
> parameters par_all27_prot_na.inp # parameter file (CHARMM)
> paratypecharmm on # (on or off) or (yes or no)
> #binvelocities md018_rst.vel
> #bincoordinates md018_rst.coor
>
> # output files
> outputname min_out
> binaryoutput no
> restartname min_rst
> restartfreq 600
> binaryrestart yes # default
> dcdfile min_traj.dcd
> dcdfreq 600
> dcdunitcell no # 'yes' is default if periodic cell is used
> veldcdfile min_traj.vel
> veldcdfreq 600
>
> # standard output
> outputenergies 600
> outputmomenta 600
> outputpressure 600
> outputtiming 600
>
> # Temperature control
> # Langevib dynamics parameters
> #langevin on
> #langevintemp 300.0
> #langevindamping 5.0
> #
> #langevinpiston on # NVT(off), NPT(on)
> #langevinpistontarget 1.0
> #langevinpistonperiod 200.0
> #langevinpistondecay 100.0
> #langevinpistontemp 300.0
>
>
> minimization on
> numsteps 2400
>
>
>
>
>
>
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