I understand where your concern is coming from now. Indeed, in the implicit solvent CpHMD Amber tutorial there is an equilibration with CpHMD active. In explicit solvent CpHMD, after the NPT equilibration with no CpHMD, you may perform another equilibration at NVT with CpHMD active before the production phase. You will find previous works with CpHMD in the literature that have done that.
I suggest you to take a look at previous constant pH papers, so you can have an idea about the simulation protocols. Here are some suggestions:
https://pubs.acs.org/doi/10.1021/ct401042b
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002761
https://pubs.acs.org/doi/10.1021/acs.jpcb.9b03816
https://pubs.acs.org/doi/abs/10.1021/jacs.9b11433
In addition to that, I suggest you to take a look at the cphstats functionalities (cphstats --help, and also at the Amber manual). There are features in there to help you evaluate the convergence of your CpHMD simulations.
I am sorry I misunderstood your initial question. I understood you were referring only to the explicit solvent CpHMD tutorial.
Best,
Vinícius Wilian D. Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Sent: Friday, September 18, 2020 9:43 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] constant pH MD in explicit solvent
[External Email]
Dear Vinicius,
So I don't have to activate constant pH during equilibration except for
production. As in implicit solvent, they use icnstph keyword and in the
command line, -cprestrt flag has been used. So as per your suggestion, I
don't need any new .cpin file for the production run at the end of
equilibration in explicit solvent (the previous .cpin file will serve the
purpose). Am I getting it right??
with regards,
Satyajit Khatua
Message: 3
Date: Mon, 14 Sep 2020 15:48:45 +0000
From: "Cruzeiro,Vinicius Wilian D" <vwcruzeiro.ufl.edu>
Subject: Re: [AMBER] constant pH MD in explicit solvent
To: "amber.ambermd.org" <amber.ambermd.org>
Message-ID:
<
MWHPR2201MB17577514D81B69E2417CB7A8D1230.MWHPR2201MB1757.namprd22.prod.outlook.com
>
Content-Type: text/plain; charset="iso-8859-1"
Hello Satyajit,
can you check if I have to add anything other than icnstph in my
equilibration input?
You should not activate constant pH during your equilibration, only during
production. As the tutorial shows, production should be executed in the NVT
ensemble.
Best,
Vin?cius Wilian D. Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Sent: Monday, September 14, 2020 3:13 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] constant pH MD in explicit solvent
[External Email]
Dear Vinicius,
Sorry for the late reply. Thanks a lot for replying as
I didn't have any clue about what to do next. I have mentioned earlier that
I have followed the explicit solvent CpHMD tutorial from the Wikidot page
demonstrated by J. Swails and in there, the equilibration step doesn't
contain the keyword as icnstph. Being new to do this simulation, I have
followed the exact keywords for the trial run and got panicked about the
unavailability of .cprestrt file and thought that maybe I have done
something wrong during system preparation or given the wrong command line
inputs. Now I definitely try what you have suggested. Another thing can you
check if I have to add anything other than icnstph in my equilibration
input?? I am attaching the input file below.
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,
/
Thanks in advance,
Satyajit
Message: 11
> Date: Sat, 5 Sep 2020 17:22:53 +0000
> From: "Cruzeiro,Vinicius Wilian D" <vwcruzeiro.ufl.edu>
> Subject: Re: [AMBER] constant pH MD in explicit solvent
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <4A2AF71A-67F9-47E1-8CAD-EFF5D01D8B02.ufl.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hello Satyajit,
>
> I am sorry your email has not been answered before.
>
> Some more information is needed in order to understand your problem
> better. Did you get an error in your NPT equilibration simulation? In the
> tutorial, constant pH MD is not performed during equilibration. It is only
> performed during the production phase of the simulation, which is ran in
> NVT. Thus, if icnstph is not set in your mdin file (or if it is set to 0),
> then you should not expect a cprestrt file.
>
> I hope this helps,
>
>
> Vin?cius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633<tel:+1(352)846-1633>
>
> On Sep 5, 2020, at 12:16 AM, SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
> wrote:
>
> ?[External Email]
>
> Dear Users,
> I had raised a ticket regarding this problem that I
> faced dated back to march 7th, 2020. Unfortunately, I couldn't able to
> solve the problem till now and also didn't get any suggestions from any
> users. So, I am mailing again to grab the user's attention in this regard.
> Please help.
>
> Thanks in advance,
> Satyajit
>
>
> Message: 4
> Date: Sat, 7 Mar 2020 12:44:32 +0530
> From: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
> Subject: [AMBER] Unavailability of the file related to -cprestrt flag
> in equilibration (NPT) step of constant pH MD in Amber14 with
> AmberTools15
> To: amber.ambermd.org
> Message-ID:
> <CAOoM83scVpX5C-hpBf==TneX4Rm5f4tesWe=97e4+bZCmdjqfw.mail.gmail.com
> >
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Users,
> I am doing a const pH MD simulations of an enzyme in
> explicit solvent and I have followed this tutorial
>
>
https://urldefense.proofpoint.com/v2/url?u=http-3A__jswails.wikidot.com_explicit-2Dsolvent-2Dconstant-2Dph-2Dmd&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=nGOAUe2dULeQMc_syIjuWyamMitar9rjTqwfSnfp6B8&s=mHiKbnmnmo75XQF6qavvU0wlpV72kbnC5_Xh0cuDk-g&e=
> for system
> preparation as well as for inputs. And for running simulation followed the
> tutorial provided in Amber advanced tutorials section
>
>
https://urldefense.proofpoint.com/v2/url?u=https-3A__ambermd.org_tutorials_advanced_tutorial18_section2.htm&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=nGOAUe2dULeQMc_syIjuWyamMitar9rjTqwfSnfp6B8&s=Dm2sSHxpLachnToDgApZwcKedTvp2VPPyp6OcFkW_PA&e=
.
> Up to
> heating it seems that there was no problem as it generated all required
> files without showing any kind of errors. But when I ran equilibration
> using
> NPT ensemble, there was no file which supposed to be created by -cprestrt
> flag. I have tried pmemd modules (both Cuda and Cuda.MPI) of AMBER for the
> run, however, the problem persists. Can someone tell me what I have done
> wrong here? Please help.
>
> Thanks a lot,
> Satyajit
> _______________________________________________
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Received on Fri Sep 18 2020 - 15:30:02 PDT
