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 - 05:00:03 PDT
