Hello Juraj,
Do you mean that you want to append the restart simulation outputs to the ones from your previous run? My suggestion is to restart another whole new H-REMD simulation using the final *ti.rst7 from the previous run as the new starting structure for the next run. For your following analysis stage, if you want to analyze the free energy using the edgembar module in AmberTools23, you can combine all the extracted energy info from each run and perform the analysis. Besides that, the replica exchange log file (remlog) cannot be restarted at the moment, which still requires another set of output files.
I notice that you are using dt=1fs, if you intend to run the H-REMD simulation longer, you may want to increase it to 4fs (with hydrogen-mass repartitioning) and some suggested changes to consider:
1. use parmed to turn on HMR for the unisc.parm7
2. change dt to 0.004
3. you can delete the "noshakemask" flags
Hope this helps!
Shi
________________________________
From: Daniel Roe via AMBER <amber.ambermd.org>
Sent: Tuesday, October 10, 2023 8:59 AM
To: Juraj Dobias <juraj.dobias.uochb.cas.cz>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] restart H-REMD simulation
Hi,
On Tue, Oct 10, 2023 at 2:54 AM Juraj Dobias via AMBER
<amber.ambermd.org> wrote:
> According to manual T-REMD can be restarted using -A flag instead of -O,
> but amber does not recognize -A flag. I tried changing starting rst7
> file in groupfile, but all output files were overwritten. I need to
> append new data to existing mdout file for subsequent analysis.
In the groupfile you posted, you have -O flags set, not -A. I think
you also might need to make sure you don't have -O specified on the
command line itself.
However, my advice is to just avoid -A altogether. Just restart from
your old run and write to a new set of files. Personally, when I'm
running REMD or any other ensemble type jobs, I put separate runs in
their own directories, e.g.
run.000
run.001
run.002
etc
This provides a nice logical separation and ensures no one file gets
too big and unwieldy. Hope this helps,
-Dan
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Received on Tue Oct 10 2023 - 16:30:02 PDT
