From: Akshay Bhatnagar (akshaybhatnagar2790_at_gmail.com)
Date: Fri Jun 06 2014 - 21:15:30 CDT
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
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> 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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