AW: Reg: deformation of water box during equilibration

From: Norman Geist (
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: [] Im Auftrag von Akshay Bhatnagar
Gesendet: Samstag, 7. Juni 2014 04:16
An: Aron Broom
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 <> 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 <> 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
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