Hello VinÃcius,
Thank you very much for your detailed help. I much appreciate your reply.
To answer your question I am interested in (1) (describing some structural
property of my system at a single value of pH).
With regards,
Saikat
On Fri, Jul 6, 2018 at 5:29 PM, Cruzeiro,Vinicius Wilian D <
vwcruzeiro.ufl.edu> wrote:
> Hello Saikat,
>
>
> Are you interested on:
>
> 1) describing some structural property of your system at a single value of
> pH?
>
> 2) describing pKa values or a pH-dependent property (like a conformational
> change)?
>
>
> If the answer is 2, you should use pH-REMD instead of T-REMD with CpHMD.
> Simulations at different pH values are important for proper description of
> case 2.
>
>
> I answer below your questions, in case you wanna do T-REMD with CpHMD.
>
>
> 1. Should I use -rem = 1 for my simulations?
>
>
> Correct.
>
> 2. In the remd.groupfile should I specify unique cpout filename for each
> replica?
>
>
> Correct.
>
> 3. After the run does the cpout file (e.g remd.cpout.001) contains the
> protonation states for lowest temp trajectory? Or do I need to process
> cpout files like we process all trajectory files to extract a particular
> temp trajectory?
>
>
> You would need to process the cpout files to sort them by target
> temperature. In Amber18 this is now trivial to do (a new AmberTool called
> fixremdcouts.py does it easily for you, but the cpout format for REMD
> simulations in Amber18 is different than in Amber12). I suppose that for
> the paper you mentioned the code was modified to print the target
> temperature to the cpout file so that it could be sorted afterwards. I
> can't imagine how you can do this with Amber12 without modifying the code.
>
>
> I hope this helps,
>
> All the best,
>
>
> VinÃcius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633
>
>
> ________________________________
> From: Saikat Dutta chowdhury <pbr322.dutta.gmail.com>
> Sent: Friday, July 6, 2018 6:52 AM
> To: AMBER Mailing List
> Subject: [AMBER] Need help regarding CpHMD with T-REMD
>
> Dear AMBER Users,
>
> I am trying to do a constant pH MD combined with T-REMD as described in
> here:
>
> "Meng, Y., & Roitberg, A. E. (2010). Constant pH replica exchange molecular
> dynamics in biomolecules using a discrete protonation model. *Journal of
> chemical theory and computation*, *6*(4), 1401-1412."
>
> I am using Amber12 for the proposed simulation.
> While trying to set up the system I am having few doubts. It would be very
> very helpful if someone can clear my doubts and point me in the right
> direction.
>
> My doubts are:
>
> 1. Should I use -rem = 1 for my simulations?
> 2. In the remd.groupfile should I specify unique cpout filename for each
> replica?
> 3. After the run does the cpout file (e.g remd.cpout.001) contains the
> protonation states for lowest temp trajectory? Or do I need to process
> cpout files like we process all trajectory files to extract a particular
> temp trajectory?
>
> With regards,
>
> Saikat Dutta Chowdhury
> Email: pbr322.dutta.gmail.com
> Mob:
> 8017650842
> 9681144106
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--
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
Mob:
8017650842
9681144106
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Received on Mon Jul 09 2018 - 08:00:02 PDT
