AW: Reg: movement of protein outside box

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Jun 13 2014 - 03:09:20 CDT

I still do not know where you expect a problem. Please understand the periodic boundary condition. It doesn’t matter where the amino acid is in the cell, it can’t leave the cell and it is always surrounded by water. If you want to have it visualized in the middle of the cell, that’s a different thing and can be done with the pbc command I already gave you.

 

Looks like a NPT run, so it can be called equilibration. But why are you using such large settings for langevinpistondecay and period? Also your restartfreq is way too low, why do u want to save a restart every (approximately) 2 minutes which are taken to do 1000 steps of md?

 

Norman Geist.

 

Von: Akshay Bhatnagar [mailto:akshaybhatnagar2790_at_gmail.com]
Gesendet: Freitag, 13. Juni 2014 09:25
An: Norman Geist
Betreff: Re: namd-l: Reg: movement of protein outside box

 

Hello sir

I have tried by enabling ZeroMomentum and switching off the COMmotion

(default), but still the amino acids moves almost out of the water box. what should I do now , so that the amino acid does not move outside the box. Also, now i am very confused between equilibration and production run. from the below configuration file can you please tell me that i am doing equilibration or production run? please.

# Input
structure /.../cystine_30.psf
coordinates /.../cystine_30.pdb
bincoordinates /.../cystine_30wb_min.coor
extendedSystem /.../cystine_30wb_min.xsc

set temperature 310
set outputname cystine_30wb_eq

firsttimestep 0
paraTypeCharmm on
parameters /namd-tutorial-files/common/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
margin 2.5
zeroMomentum yes

# Integrator Parameters
timestep 1 ;# 1 fs/step
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

#manual grid definition
PMEGridSizeX 38
PMEGridSizeY 38
PMEGridSizeZ 38

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

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 1000000.0
langevinPistonDecay 500000.0
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 1000
outputPressure 1000

run 10000000 ;# equilibration run for 1ns

Thank you very very much!

With Regards

Akshay Bhatnagar

PhD Student

BITS Pilani Hyderabad Campus

 

 

On Tue, Jun 10, 2014 at 5:56 PM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:

As long as there’s no constant linear momentum, I guess there’s no problem, simply Brownian motion. Otherwise it may be effects like “center of mass drift” due long range electrostatics (PME) which represents a high center of mass motion. This can be controlled by the namd options “zeromomentum” and “commotion”.

 

Norman Geist.

 

Von: Akshay Bhatnagar [mailto:akshaybhatnagar2790_at_gmail.com]

Gesendet: Dienstag, 10. Juni 2014 14:19
An: Norman Geist

Betreff: Re: namd-l: Reg: movement of protein outside box

 

Thank you very much for your suggestions and kind help

But, in my system, the amino acid i am simulating is there at the center position already which i checked through the command "measure center $protein" and so is the water box. so, should i use the “pbc wrap –all –compound res –center com –centersel protein”? , Also I wanted to ask that is this diffusion a normal process after equilibration or is it due to bad system or bad parameters in the configuration file. Actually what could be the reason for diffusion if the system is already at the origin position.

 

Thanking you

With Regards

Akshay Bhatnagar

PhD Student

BITS Pilani Hyderabad Campus

 

 

On Tue, Jun 10, 2014 at 1:17 PM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Akshay Bhatnagar
Gesendet: Dienstag, 10. Juni 2014 03:47
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Reg: movement of protein outside box

 

Hello everyone

 

I have performed a 10 ns equilibration to simulate a amino acid in a 30 A water box, but after the equilibration the amino acid has moved to the corner of the box. can anyone explain me the reason?

 

Diffusion. If you wan’t to have it in the middle of the box, see in VMD “pbc wrap –all –compound res –center com –centersel protein”. Please notice that the

Center of the box can be everywhere you want.

 

Also can anyone tell me the exact difference between equilibration and production run? If I use pressure control parameter in equilibration then is it equivalent to production run?

 

During equilibration you usually have: restraints, temperature control, pressure control … (see NVT,NPT)

During production run you usually have no external controls of your simulation. (see NVE)

 

Thank you very much

With Regards

Akshay Bhatnagar

PhD Student

BITS Pilani Hyderabad Campus

 

 

 

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