Re: Reg: deformation of water box during equilibration

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Sat Jun 07 2014 - 05:05:35 CDT

Akshay,

Just try to make system with PBC dimensions closer to PME grid size. If
you run simulation of cysteine, suppose that amino-acid is in its
zwitterionic form and that you have no counterions or similar in the
system. Also, after solvation of amino-acid check visually is solvation
sphere (water box) looks equilibrated or not (can you see the 'plane'
without water molecules between 'planes' of water molecules when rotate
the system in the graphical user interface). It is good practice to have
prepared equlibrated water cluster for solvation purposes.

Branko

On 6/7/2014 4:15 AM, Akshay Bhatnagar wrote:
> 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/cm^3.
> 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
> 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 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
> <mailto: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
> <mailto: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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