Hi
The tutorials, like all our tutorials, are not general recipes but
rather a way to teach the techniques.
In your case, if you are new to amber, I would suggest running some
simpler simulations first to get your feet wet.
As for your direct question:
This is the input file in the tutorial:
Implicit solvent constant pH initial heating mdin
&cntrl
imin=0, irest=0, ntx=1,
ntpr=500, ntwx=500, nstlim=1000000,
dt=0.002, ntt=3, tempi=100,
temp0=300, tautp=2.0, ig=-1,
ntp=0, ntc=2, ntf=2, cut=30,
ntb=0, igb=2, tol=0.000001,
nrespa=1, saltcon=0.1,*icnstph=1*,
*solvph=7.5, ntcnstph=100000000*,
gamma_ln=5.0, ntwr=500, ioutfm=1,
nmropt=1, ntr=1, restraint_wt=2.0,
restraintmask='.CA,C,O,N',
/
&wt
TYPE='TEMP0', ISTEP1=1, ISTEP2=500000,
VALUE1=10.0, VALUE2=300.0,
/
&wt TYPE='END' /
I put 3 variables in bold
icnstph=1 means DO constant ph in implicit solvent
solvph=7.5 means try a ph 7.5
ntcnstph = 100000000 means try to change protonation states every those
steps, which are set equal to 10 x nstlim.**This means that amber will
never really try to change protoation states, and will stay at your
initial setting for that.
For the second question, the setting of 4.5 was an initial setup, so you
can be ready to do other phs later on.
If all you want if a single pH, by all means use that throughout.
Adrian
*
*
On 3/11/21 11:00 AM, Abhik Ghosh Moulick wrote:
> [External Email]
>
> Dear There,
> I am new in amber. I am trying to run constant ph molecular dynamics
> simulation in implicit solvent. I am following the tutorial given in amber
> website. I have some confusion. At first section 2 during heating of the
> system (https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_advanced_tutorial18_files_heat.mdin&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=6m9itdHniQ3zNalYxdFWOb6qoOAOSuEW_VhkbqGjMrs&s=ZONzf_yihAw6wQy0N0oqOs6SgxRdEJz0NybZicTGX0Q&e= )
> they are putting solvent ph to 7.5. I have not understood why they are
> heating the system with solvent ph 7.5. If I want to perform simulation in
> constant ph 1 or 2, is it necessary to keep solvent ph 7.5 during the
> heating step? Secondly at step 3 at first they do the equilibration at
> constant ph 4.5 and then perform simulation at various ph using output of
> the simulation run at ph 4.5. In my case, if I want simulation at ph 2
> then should I put ph value 2 at all the time?
> Thanks in advance.
> Best Regards
> ABhik
>
>
>
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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Mar 11 2021 - 08:30:03 PST
