[AMBER] constant pH MD in explicit solvent

From: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Date: Fri, 18 Sep 2020 19:13:58 +0530

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>

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


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
   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,

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
> for system
> preparation as well as for inputs. And for running simulation followed the
> tutorial provided in Amber advanced tutorials section
> 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 - 07:00:02 PDT
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