From: Christopher Gillespie (gillescche_at_gmail.com)
Date: Thu Mar 05 2009 - 12:04:02 CST
Hi Brittany,
I had a similar problem once and once I removed the "auto none"
everything was fine.
Chris
On Mar 5, 2009, at 8:56 AM, Brittany Morgan wrote:
> Hi Chris,
>
> Here is the psfgen input script:
>
> topology /home/brittanym/topparnew/top_all27_p_n_new.inp
>
> pdbalias residue HIS HSD
>
> pdbalias atom MET H HN
> pdbalias atom MET HB2 HB1
> pdbalias atom MET HB3 HB2
> pdbalias atom MET HG2 HG1
> pdbalias atom MET HG3 HG2
>
> pdbalias atom GLN H HN
> pdbalias atom GLN HB2 HB1
> pdbalias atom GLN HB3 HB2
> pdbalias atom GLN HG2 HG1
> pdbalias atom GLN HG3 HG2
>
> pdbalias atom LYS H HN
> pdbalias atom LYS HB2 HB1
> pdbalias atom LYS HB3 HB2
> pdbalias atom LYS HD2 HD1
> pdbalias atom LYS HD3 HD2
> pdbalias atom LYS HE2 HE1
> pdbalias atom LYS HE3 HE2
> pdbalias atom LYS HG2 HG1
> pdbalias atom LYS HG3 HG2
>
> pdbalias atom GLY H HN
> pdbalias atom GLY HA2 HA1
> pdbalias atom GLY HA3 HA2
>
> pdbalias atom ASN H HN
> pdbalias atom ASN HB2 HB1
> pdbalias atom ASN HB3 HB2
>
> pdbalias atom PHE H HN
> pdbalias atom PHE HB2 HB1
> pdbalias atom PHE HB3 HB2
>
> pdbalias atom ARG H HN
> pdbalias atom ARG HB2 HB1
> pdbalias atom ARG HB3 HB2
> pdbalias atom ARG HD2 HD1
> pdbalias atom ARG HD3 HD2
> pdbalias atom ARG HG2 HG1
> pdbalias atom ARG HG3 HG2
>
> pdbalias atom THR H HN
> pdbalias atom ALA H HN
> pdbalias atom VAL H HN
>
> pdbalias atom CYS H HN
> pdbalias atom CYS HB2 HB1
> pdbalias atom CYS HB3 HB2
>
> pdbalias atom GLU H HN
> pdbalias atom GLU HB2 HB1
> pdbalias atom GLU HB3 HB2
> pdbalias atom GLU HG2 HG1
> pdbalias atom GLU HG3 HG2
>
> pdbalias atom HIS H HN
> pdbalias atom HIS HB2 HB1
> pdbalias atom HIS HB3 HB2
>
> pdbalias atom ILE H HN
> pdbalias atom ILE CD1 CD
> pdbalias atom ILE HG12 HG11
> pdbalias atom ILE HG13 HG12
> pdbalias atom ILE HD11 HD1
> pdbalias atom ILE HD12 HD2
> pdbalias atom ILE HD13 HD3
>
> pdbalias atom PRO HB2 HB1
> pdbalias atom PRO HB3 HB2
> pdbalias atom PRO HD2 HD1
> pdbalias atom PRO HD3 HD2
> pdbalias atom PRO HG2 HG1
> pdbalias atom PRO HG3 HG2
>
> pdbalias atom TRP H HN
> pdbalias atom TRP HB2 HB1
> pdbalias atom TRP HB3 HB2
>
> pdbalias atom ASP H HN
> pdbalias atom ASP HB2 HB1
> pdbalias atom ASP HB3 HB2
>
> pdbalias atom SER H HN
> pdbalias atom SER HB2 HB1
> pdbalias atom SER HB3 HB2
> pdbalias atom SER HG HG1
>
> pdbalias atom LEU H HN
> pdbalias atom LEU HB2 HB1
> pdbalias atom LEU HB3 HB2
>
> pdbalias atom TYR H HN
> pdbalias atom TYR HB2 HB1
> pdbalias atom TYR HB3 HB2
>
> segment VTS {pdb VTS_U.pdb; first NONE; last CTER; auto none}
> coordpdb VTS_U.pdb VTS
>
> writepsf VTSU.psf
> writepdb VTSU.pdb
>
>
>
>
>
>
> The NAMD configuration file:
>
>
> structure /home/morganb/vtsu/vtsu.solv.psf
> coordinates /home/morganb/vtsu/vtsu.solv.pdb
> outputName ./min/vts.output
>
> set temperature 298
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters /home/morganb/par_all27_p_n_new.inp
>
> # NOTE: Do not set the initial velocity temperature if you
> # have also specified a .vel restart file!
> temperature $temperature
>
>
> # Periodic Boundary conditions
> # NOTE: Do not set the periodic cell basis if you have also
> # specified an .xsc restart file!
> if {1} {
> cellBasisVector1 54. 0. 0.
> cellBasisVector2 0. 54. 0.
> cellBasisVector3 0. 0. 54.
> cellOrigin 0.35 -0.93 1.59
> }
> wrapWater on
> wrapAll on
> zeroMomentum no ; #can use for NVE
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 0.5 ;# 2fs/step
> #rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 1
> stepspercycle 10
>
>
> #PME (for full-system periodic electrostatics)
> if {1} { # For speed, grid sizes should only have factors of 2, 3
> and 5
> PME yes
> PMEGridSizeX 54
> PMEGridSizeY 54
> PMEGridSizeZ 54
> PMEGridSpacing 1.0
> }
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
>
>
> # Constant Pressure Control (variable volume)
> if {1} {
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell no ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, yes for membrane
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
> }
>
>
> restartfreq 2000 ;# 500steps = every 1ps
> dcdfreq 100
> xstFreq 2000
> outputEnergies 100
> outputPressure 100
> #velDCDfreq 100
>
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> if {1} {
> minimize 5000; # Number of force evaluations
> reinitvels $temperature
> }
>
> run 0;
>
>
>
>
>
>
>
> From: charris5_at_gmail.com [mailto:charris5_at_gmail.com] On Behalf Of
> Chris Harrison
> Sent: Wednesday, March 04, 2009 8:41 PM
> To: Brittany Morgan
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: Minimization convergence issue
>
> If you are using a script as input to psfgen, can you paste the
> script in a reply email? Can you also paste the namd configuration
> file. Sounds like something could be wrong with angle, vdW, etc
> definitions in the psf or parameters read-in during NAMD's startup.
>
>
> C.
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>
>
>
----------------------------------------------------------------------------------------
| Christopher Gillespie
| Ph.D. Candidate
| University of Delaware
| Department of Chemical Engineering
| 150 Academy Street
| Newark, DE 19716
| gillesc (at) udel.edu
| http://udel.edu/~gillesc
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