AW: Reg: deformation of water box during equilibration

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
 
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