From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jun 10 2014 - 02:23:04 CDT
What do you mean with „deformation”. As I can’t see any barostat settings in your config, your box size and ratio CAN’T be changed by the simulation you sent the config of. Also see comments below:
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Akshay Bhatnagar
Gesendet: Samstag, 7. Juni 2014 04:16
An: Aron Broom
Cc: namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: Reg: deformation of water box during equilibration
yes i have checked. it has been mentioned that this occurs due to density problems. but the water box i am using is having 1.0 gm/cm3. still the shape is getting deformed. the configuration is below :
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
# Integrator Parameters
timestep 0.5 ;# 0.5 fs/step
As far as I know, timesteps lower 1 can’t be used, see log file.
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 35.0 0.0 0.0
cellBasisVector2 0.0 35.0 0.0
cellBasisVector3 0.0 0.0 35.0
cellOrigin 0.0 0.0 0.0
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
It’s useless to use both pmegridspacing and pmegridsize(X,Y,Z)
#manual grid definition
PMEGridSizeX 40
PMEGridSizeY 40
PMEGridSizeZ 40
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 500
outputPressure 500
run 5000000 ;# equilibration run for 10ns
With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus
On Fri, Jun 6, 2014 at 11:07 PM, Aron Broom <broomsday_at_gmail.com> wrote:
did you search through the mailing list archives? This question is asked often, and usually has the same solution.
On Fri, Jun 6, 2014 at 12:35 PM, Akshay Bhatnagar <akshaybhatnagar2790_at_gmail.com> wrote:
Hello everyone
I wanted to simulate cystine in a 30 A box but after the equilibration the
water box shape is deformed. I am not understanding why it happened as i
have given PME boundaries. can anyone suggest me the possible sources of errors?
Please help!!
With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo --- Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv. http://www.avast.com
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