From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Thu Oct 15 2009 - 10:22:44 CDT
Guys, thanks for replies,
1) yes i wrap all
2) why 2 fs is an aggressive timestep. i thought the larger the system
the more applicable is this timestep, because we don't care about high
frequency motion.
3) center of mass drifts a _little bit_; is it that bad taking into
account that box expands eventually to 5000 A and center of mass moved
mere 170 A; here is center of mass of the system from complete
trajectory:
0.140819340045 <- box size 151 A
0.198334947494
0.288038157328
0.19873215805
0.286829637933
0.186835462234
0.275995509843
0.434466743708
0.497470887712
0.658240068259
0.793976753539
0.815130443344
0.852871757556
0.974599044064
0.793144207418
0.730648404732
0.594386321733
0.499312609197
0.39109067872
0.353292350317
0.300058418619
0.860983950507
0.268274330197
0.787020802622
1.72985920819
2.27208377526
2.56290788922
2.95070511197
3.10428896559
10.9796880961
92.459702794
167.948345538
174.430522239
171.411847346 <---- box size around 5000A
4) I wonder why people who did DNA translocation don't reply. Am i the
only one who set up simulation system incorrectly? :)
5) here is namdconf :
--------------------------------------------------------------------------------------------------------------------------------------
eFieldOn yes
eField 0 0 1
wrapAll on
PME yes
PMEGridSizeX 176
PMEGridSizeY 176
PMEGridSizeZ 120
fixedAtoms off
fixedAtomsFile pdb-fixed/trans-dna35b.pdb
fixedAtomsCol B
#############################################################
## ADJUSTABLE PARAMETERS ##
structure psf-wb/trans-dna35b.psf
coordinates psf-wb/trans-dna35b.pdb
set temperature 310
#equilibrated for 5000 and copied to psf-wb/
set run_steps 3000000
set outputname trans-dna35b
#firsttimestep 0
binCoordinates trans-dna35b.restart.coor
extendedSystem trans-dna35b.restart.xsc
binaryoutput no
#############################################################
## SIMULATION PARAMETERS ##
# Input
paraTypeCharmm on
parameters /users/rpetrenk/bin/par_all27_prot_lipid_na.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 5000 ;# 500steps = every 1ps
dcdfreq 5000
xstFreq 5000
outputEnergies 5000
outputPressure 5000
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
reinitvels $temperature
langevinTemp $temperature
run $run_steps ;# 5ps
On Thu, Oct 15, 2009 at 11:01 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> roman,
>
>> In other runs with exactly the same system but 10 times smaller
>> electric field 4.4 ns of simulations are as expected.
>>
>> Should it explode when 10 ns is reached? Has anyone observed system
>> explosion _after_ the system is minimized and partially equilibrated?
>
> please consider that you are using a pretty aggressive time step
> and that increasing the external field will add a constant term to
> the forces on charged atoms. it could just be that your integration
> has become unstable.
>
> independent of that, have you checked how much of a center of mass
> drift you get?
>
> cheers,
> axel.
>
>>
>> --
>> Roman Petrenko
>> Physics Department
>> University of Cincinnati
>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
-- Roman Petrenko Physics Department University of Cincinnati
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