Dear George,
The equilibration described on Jason's tutorial is actually just a simple NPT simulation with no constant pH (that is why the icnstph flag is not being set on equil.mdin). The intent of this equilibration is not only to relax the system at the target temperature, but also to get a box with the proper density for the NVT production simulation with constant pH. If you have a large number of water molecules in your box, the density should converge to a value close to 1.000 at the NPT simulation. You may check if that is happening on the mdout file of the equilibration simulation. If the density is not converged, you should run it again and longer.
Therefore, on Jason's tutorial, we only expect the cpin file to be taken into consideration and the cpout and cprestrt files to generated at the production simulation.
I hope this helps,
Regards,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: George Tzotzos <gtzotzos.me.com>
Sent: Sunday, September 3, 2017 7:57:44 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Explicit solvent CpHMD: seeking clarifications
Thank you Jason.
The equil.mdin I used is, as per your Wikidot page:
Explicit solvent molecular dynamics constant pressure MD
&cntrl
imin=0, irest=1, ntx=5,
ntpr=1000, ntwx=1000, nstlim=2000000,
dt=0.002, ntt=3, tempi=300,
temp0=300, gamma_ln=1.0, ig=-1,
ntp=1, ntc=2, ntf=2, cut=8,
ntb=2, iwrap=1, ioutfm=1,
/
I don’t see icnstph=2 in the above script. Have I missed something?
I checked the mail archive and found that the same problem was reported:
http://archive.ambermd.org/201702/0173.html <
http://archive.ambermd.org/201702/0173.html>
There’s an answer by Eric Lang. I’m not sure how to interpret it as I think that the equil.cpin file is needed for the production MD.
Regards
George
> On 3 Sep 2017, at 14:42, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Sat, Sep 2, 2017 at 1:07 PM, George Tzotzos <gtzotzos.me.com <mailto:gtzotzos.me.com>> wrote:
>
>> It’s my first attempt at explicit solvent CpHMD. In summary, my objective
>> is to predict whether structural changes of a protein-ligand complex
>> brought about by changes in pH result in the release of the ligand. I
>> intend to perform simulations at pHs 5, 6 and 7.
>>
>> As a starting point, I’m using the same md.in files described in
>> http://jswails.wikidot.com/explicit-solvent-constant-ph-md <
>> http://jswails.wikidot.com/explicit-solvent-constant-ph-md <http://jswails.wikidot.com/explicit-solvent-constant-ph-md>>
>>
>> I’ve successfully generated protein_solv.cpin which I then used in heating
>> and equilibrating the system using the following input commands:
>>
>> (heat) $PMEMD -O -i heat.in -c subA.min.rst -p subA_solv.modO.prmtop -ref
>> subA.min.rst -cpin subA_solv.cpin -o subA.heat.out -r subA.heat.rst -x
>> subA.heat.nc
>>
>> (equilibration) $PMEMD -O -i equil.in -p subA_solv.modO.prmtop -c
>> subA.heat.rst -cpin subA_solv.cpin -o subA.equil.out -cpout
>> subA.equil.cpout -r subA.equil.rst -x subA.equil.nc -cprestrt
>> subA.equil.cpin
>>
>> In the equilibration step, I obtained the equil.out, equil.cpout,
>> equil.rst, and equil.nc but NOT the expected equil.cpin
>>
>
> If you used the mdin file from my Wikidot page for equilibration, then you
> never set icnstph=2. This means that the equilibration was *not* run at
> constant pH, so no cprestart will be created (although no cpout should have
> been created either).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Sun Sep 03 2017 - 06:30:02 PDT
