Yes that's what I mean. But do make sure you aren't restraining everything,
or you won't sample different coordinates for different Hs.
On Thu, Sep 26, 2024, 6:14 PM Liyanage, Risi (MU-Student) <
rrlnhq.missouri.edu> wrote:
> By reference structure do you mean the input for the -ref flag? I have
> tried using the crd s of the first replica as the -ref input for all
> replicas. It works. Thank you!
>
> Sent from Outlook for Android <https://aka.ms/AAb9ysg>
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Thursday, September 26, 2024 4:53:45 PM
> *To:* Liyanage, Risi (MU-Student) <rrlnhq.missouri.edu>
> *Cc:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* Re: [AMBER] Calculating the number of replicas for h-remd
>
> It can be very sensitive to the restraints. you need to use the exact same
> reference structure for every replica, but that may not be enough. Start
> with that if you didn't already.
>
> On Thu, Sep 26, 2024, 5:35 PM Liyanage, Risi (MU-Student) <
> rrlnhq.missouri.edu> wrote:
>
> Dear professor,
>
> Thank you very much for the valuable solution. With no cartesian
> restraints, replicas do exchange as intended. Original system had 2
> kcal/mol cartesian restraints on protein. I have tried lowering the
> restraint_wt and reducing the number of atoms in mask which has led to
> workable combination. Still, I would like to know, can there be any
> workarounds for this issue without having to use said remedies?
>
> Sent from Outlook for Android <https://aka.ms/AAb9ysg>
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Monday, September 23, 2024 1:48:09 PM
> *To:* Liyanage, Risi (MU-Student) <rrlnhq.missouri.edu>
> *Cc:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* Re: [AMBER] Calculating the number of replicas for h-remd
>
> I would try turning off restraints, especially Cartesian. See if the
> exchange improves as a way of debugging the issue. These can be tricky in
> hremd. If it fixes the problem, then you can see how to improve them.
>
> On Mon, Sep 23, 2024, 2:28 PM Liyanage, Risi (MU-Student) <
> rrlnhq.missouri.edu> wrote:
>
> Dear professor Carlos,
> Thanks for the reply.
> Yes, I am applying a harmonic restraint along the reaction coordinate in
> each replica (same anchor strength, anchor position changes). I have
> attached the colvar files to this email.
> This is a CRISPR system and has both protein and nucleic acid parts. I
> have used positional restraints on proteins and used distance restraints at
> the ends of the nucleic acid helices to prevent basepair fraying at
> terminals. I assumed it would not be an issue since they are the same for
> each replica, but maybe I am wrong.
> I have conducted nvt ensemble (no replica exchange) runs on a 4-replica
> system and looked at the reaction coordinate overlapping over time. They
> overlap very well. (I have attached the output files of this simulation)
> In order to reduce the gap between the PotE(x_1) and PotE(x_2) columns I
> have tried changing the spacing, changing the force constant but to no
> avail. I have attached the input and restraints files if needed. If I am
> correct PotE(x_1) contains the energies of the current replicas and
> PotE(x_2) contains the target energies. Current potential energies seem to
> be very close to each other, yet the target energy differ by a large amount
> form the current energy and exchange won't take place. (rem.log attached)
> How am I to get these two energies closer to each other? Thanks in advance
> for any ideas on this.
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Saturday, September 21, 2024 6:36 AM
> *To:* Liyanage, Risi (MU-Student) <rrlnhq.missouri.edu>; AMBER Mailing
> List <amber.ambermd.org>
> *Subject:* Re: [AMBER] Calculating the number of replicas for h-remd
>
> WARNING: This message has originated from an External Source. This may be
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> clicking links, or responding to this email.
> What is the difference in hamiltonians between neighboring replicas? You
> mention reaction coordinate, are you changing the position of a harmonic
> restraint? If yes, then the force constant is also important in addition to
> spacing.
> Look at the energy difference reported in the output you sent, it is very
> large. Does that make sense? Setting up these simulations can be tricky,
> and needs information that only you know. It also takes a good
> understanding of the principles behind HREMD, and how the exchange works.
> You might start by calculating the reaction coordinate value vs time for
> each replica, making a histogram, and seeing if they have overlap.
>
>
> On Fri, Sep 20, 2024, 4:34 PM Liyanage, Risi (MU-Student) via AMBER <
> amber.ambermd.org> wrote:
>
> Dear amber community,
>
> I am trying to run a h-remd for a relatively large system (60404 atoms
> after solvation). To create the replicas i have changed the distance
> between CoMs of two residues (as the reaction coordinate) and picked
> replicas from that. I have conducted the same simulation for a smaller
> system (setting 0.6 Angstrom reaction coordinate difference between each
> replica) and did not encounter any issues. But for the larger system I have
> tried, 0.1,0.2,0.3,0.4 angstrom differences but still not getting any
> replica exchanges. Infact left_fe, right_fe keep showing '-infinity'
> (picture attached). Since h-remd is said to be less dependent on the number
> of replicas (as opposed to t-remd) with the increasing system size, this
> problem is quite difficult for me to understand. Can anyone give me an idea
> about this issue or propose a way to calculate the number of replicas for
> h-remd?
>
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Received on Thu Sep 26 2024 - 15:30:02 PDT
