RE: Minimization convergence issue

From: Brittany Morgan (brmorgan_at_clarku.edu)
Date: Thu Mar 05 2009 - 12:46:28 CST

That worked. Thank you!

 

Brittany

 

  _____

From: Christopher Gillespie [mailto:gillescche_at_gmail.com]
Sent: Thursday, March 05, 2009 1:04 PM
To: Brittany Morgan
Cc: char_at_ks.uiuc.edu; namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Minimization convergence issue

 

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
 
 
 
 
 
 
 
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|  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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