Re: namd-l digest V1 #979

From: Nutan Preety (nutanpreety_at_gmail.com)
Date: Mon Feb 04 2013 - 06:18:55 CST

Hello all namd users,
I am new to namd and trying to run minimization. I increased minimization
steps to 500 to 10,000 but everytime I am getting same type of error.
please help me.

REINITIALIZING VELOCITIES AT STEP 10000 TO 310 KELVIN.
TCL: Running for 2500 steps
ERROR: Constraint failure in RATTLE algorithm for atom 593!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2049!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 570!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1167!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 73!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 10!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 170!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 185!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.

Below is the configuration file content:

# Minimization and Equilibration of
# Ubiquitin in a Water Box

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure JBP_wb.psf
coordinates JBP_wb.pdb

set temperature 310
set outputname JBP_wb_eq

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin off ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
cellBasisVector1 42.0 0. 0.0
cellBasisVector2 0.0 44.0 0.0
cellBasisVector3 0.0 0 47.0
cellOrigin -18.077 45.61 27.75

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0

#manual grid definition
#PMEGridSizeX 45
#PMEGridSizeY 45
#PMEGridSizeZ 48

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston OFF
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
binaryoutput no ;#give me the pdb instead of .coor

#############################################################
## EXTRA PARAMETERS ##
#############################################################

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
minimize 10000
reinitvels $temperature

run 2500 ;# 5ps

On Mon, Feb 4, 2013 at 12:37 PM, namd-l digest <
owner-namd-l-digest_at_ks.uiuc.edu> wrote:

>
> namd-l digest Monday, February 4 2013 Volume 01 : Number
> 979
>
>
>
> In this issue:
>
> namd-l: unsubscribe
> namd-l: unsubscribe
> namd-l: unsubscribe
> namd-l: NAMD mailing list unsubscribe instructions
> namd-l: SMD and torque application
> namd-l: unsubscribe
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> Date: Sun, 3 Feb 2013 08:38:18 -0500
> From: Purushottam Dixit <dixitpd_at_gmail.com>
> Subject: namd-l: unsubscribe
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> Date: Sun, 3 Feb 2013 22:32:28 +0530
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> Date: Sun, 3 Feb 2013 18:28:32 +0100
> From: =?UTF-8?Q?Ajasja_Ljubeti=C4=8D?= <ajasja.ljubetic_at_gmail.com>
> Subject: namd-l: NAMD mailing list unsubscribe instructions
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> ------------------------------
>
> Date: Sun, 3 Feb 2013 22:42:09 +0200
> From: "George Patargias" <gpat_at_bioacademy.gr>
> Subject: namd-l: SMD and torque application
>
> Hello
>
> I just wanted to ask how can one apply a torque to a center of mass of a
> group of atoms using the SMD module of NAMD.
>
> Do we have to define of the rotConstraints, rotConsAxis, rotConsPivot and
> rotConsVel options in the NAMD configuration file plus the SMD options?
>
> I noticed that in this link http://www.ks.uiuc.edu/Research/f1atpase/
>
> it is mentioned "We use steered molecular dynamics (SMD) simulations to
> apply a torque to F1..."
>
> Thanks.
>
> George
>
> ------------------------------
>
> Date: Mon, 4 Feb 2013 01:34:25 +0200
> From: Elif Ozkirimli <ozkiriml_at_gmail.com>
> Subject: namd-l: unsubscribe
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> End of namd-l digest V1 #979
> ****************************
>
>

-- 
Regards,
*****
Nutan Chauhan
Ph.D. Student,
Department of Biotechnology,
BIT, Mesra
Ranchi 835215
Jharkhand
INDIA

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