Okay.
Suppose if I had carried out a 10ns CpHMD run, I get .cpin file as output.
This particular output file provides the protonation state details of the
last frame, right? I, on the other hand, intend to obtain such a file for
some intermediate frame and then I want to use the same as a restart file
for some other run (*I just don't want to visualize the protonation state*).
So is it possible I can do this?
*Regards,*
*Divya Rai*
*Research Scholar*
*Department of Chemistry*
*IIT Kharagpur*
[Linkedin <
https://www.linkedin.com/in/divyaarai/>]
On Mon, 21 Nov 2022 at 21:25, Vinicius Wilian Cruzeiro <vwcruz.stanford.edu>
wrote:
> Hello Divya,
>
> When you say CPIN file for a particular frame, I suspect you refer to
> having the protonation states of that particular frame as initial condition
> in your CPIN file, is that right? If so, this is precisely what the
> CPRESTRT file does for you.
>
> Keep in mind that you can know all protonation states at any frame of your
> trajectory from the data in the CPOUT file. There is even a script that
> allows you to visualize your protonation states on VMD (see VMD_pH.py in
> https://ambermd.org/tutorials/advanced/tutorial18/section4.htm ).
>
> I hope this helps,
>
> *VinÃcius Wilian D. Cruzeiro, PhD*
> Postdoctoral Researcher
> Department of Chemistry
> Stanford University
> Twitter: .vwcruzeiro
> ------------------------------
> *From:* Divya Rai via AMBER <amber.ambermd.org>
> *Sent:* Monday, November 21, 2022 6:44 AM
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* [AMBER] Generation of CPIN in CpHMD simulations
>
> Hello everyone,
>
> I wanted to know while doing Constant pH MD simulation in explicit solvent
> whether there is anyway one can generate cpin files for a particular frame?
> Any lead would be appreciated.
>
>
> Regards,
>
> Divya Rai
> Research scholar
> IIT Kharagpur
> --
> *Regards,*
>
> *Divya Rai*
>
> *Research Scholar*
> *Department of Chemistry*
> *IIT Kharagpur*
>
> [Linkedin <https://www.linkedin.com/in/divyaarai/>]
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Received on Tue Nov 22 2022 - 03:30:02 PST
