Re: Simulation failed during the stage of heat

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Fri Mar 24 2006 - 12:29:34 CST

Hi Shulin,

Include in your conf file:

rigidbonds all

This will fix your hydrogen atoms to their mother atoms, hopefully
preventing them from moving too fast.

Regards,

Arneh

Shulin Zhuang wrote:

> Dear All,
>
> When I use namd2.6b1 at the linux cluster to heat my protein, I get a
> problem. The progein is solvated using vmd for 8 angstrom. However,
> the earlies energy minimization stage runs well , after the
> minimization stage, I run 7000 step to heat the protein. the time step
> is 2 ps. at steps 3200, the erros arise:
>
> WRITING COORDINATES TO DCD FILE AT STEP 3200
> ERROR: Atom 4361 velocity is 6301.42 17609.1 -8680.79 (limit is 5000)
> ERROR: Atom 4991 velocity is -5977.04 -16855.7 8820.4 (limit is 5000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Exiting prematurely.
>
> The atom 4361 in my protein is the HB2 of HSE residue, and 4991, HE2
> of MET residue
>
> ATOM 4361 HB2 HSE 290
> ATOM 4991 HE2 MET 329
>
> The configuration file is attached.
>
> Wish you would give me any suggestions.
>
>
>
> --
> Shulin Zhuang
> Chemistry Department
> Zhejiang University PRC
> shulin.zhuang_at_gmail.com <mailto:shulin.zhuang_at_gmail.com>
>
>------------------------------------------------------------------------
>
># NAMD configuration file for heating
># based on BPTI example in NAMD manual and apoa1.namd.
># modified by ssomani on 24 Aug, 2004
># modified by ssomani on 01 Sep, 2004 -- added MOL
>
>######################TOSET############################
># molecular system
>set MOL 2sol
>structure ${MOL}.psf
>
># after minimization
>set inprot ${MOL}_min
>coordinates ${inprot}.coor
>velocities ${inprot}.vel
>extendedSystem ${inprot}.xsc
>
>#restart previous heat run
>#coordinates kin_heat.coor
>#velocities kin_heat.vel
>#extendedSystem kin_heat.xsc
>
>set outputname ${MOL}_heat
>set heat_restart ${MOL}_heat_restart
>
>set desiredtemp 300 ;# initial temperature
>
>puts "this will go into the log file. ${inprot}.coor"
>######################TOSET############################
>
># start from 0 for heating.
># use only coordinates after em, but not velocities.
>
># force field
>paratypecharmm on
>parameters par_all22_prot.inp
>exclude scaled1-4
>1-4scaling 1.0
>
>wrapAll on
>
>PME on
>PMEGridSizeX 64 # size along cellBasisVector1.
>PMEGridSizeY 64 # along cellBasisVector2.
>PMEGridSizeZ 64
># use numbers with small integer factors: 2,3,5.
>
># approximations
>switching on
>switchdist 10
>cutoff 12
>pairlistdist 13.5
>
># center-of-mass motion is automatically removed.
>
># integrator
>timestep 2.0 # in fs.
>stepspercycle 20
>nonbondedFreq 2 # BerendsenPressureFreq takes this value.
>
># output
>outputName $outputname
>
>dcdfreq 100 ;# how often we output trajectories
>xstFreq 100
>outputEnergies 100
>outputPressure 100
>outputtiming 100
>binaryoutput no
>
># for restarting:
>restartname $heat_restart
>restartfreq 1000
>restartsave yes
>binaryrestart no ;# preserves more accuracy.
>
>#temperature 0 # sets initial temperature. use '; #' aft "run".
># disable 'temperature' when using a velocity file.
>
># For heating, use temperature reassignment.
>#reassignFreq 300 # tuned to be suit 'natural' heating for system.
>#reassignTemp 0 # to start from 0 Kelvin, else always lagging by 25K.
>#reassignIncr 25
>#reassignHold 300
>
>langevin on
>langevinTemp $desiredtemp
>langevinDamping 1.0 # mailing-list
>langevinHydrogen on
>
>
>run 7000 ; # heat for 7 ps
>
>

-- 
----------------------------
Arneh Babakhani
University of California at San Diego
Physical Chemistry / Department of Chemistry & Biochemistry
Laboratory of Prof. J. A. McCammon
9500 Gilman Drive MC 0365
La Jolla, CA 92093-0365
(619)895-6540
(858)534-4974 (FAX)
http://mccammon.ucsd.edu/~ababakha/
ababakha_at_mccammon.ucsd.edu

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