Hi,
The plot and those numbers look fairly decent to me. Your density
isn't fluctuating that much (seems to be on the order of ~0.015
amu/Ang^3) and the fit values seem to indicate the density plateaus at
around 612 ps (the pltime column) which seems right in line with how
the density behaves (initially it seems a little lower - you could
maybe plot a running average to see if that's really the case). The
actual fit parameters aren't that great but I think that's because the
density change is in fact quite small, so there isn't much relaxing
actually going on. If you're really worried you can look at things
like the total energy, temperature, RMSD to the initial structure,
etc. to see if the system really is relaxing or if there is something
else maybe going on.
If this were my data I would feel OK starting production simulations
after this, but it can't hurt to check some of the things I mentioned.
Hope this helps,
-Dan
On Sun, Aug 18, 2024 at 3:56 AM Maciej Spiegel
<maciej.spiegel.umw.edu.pl> wrote:
>
> Hi Dan,
>
> Here’s the plotted on of the Eval.agr: https://imgur.com/nNRO0Tg
> …but Eval.results doesn’t look good (?): https://pastebin.com/tnWnR5E1 It is only a single record.
> What do you think about it?
>
> Maybe this part is relevant for the output:
>
> Perhaps I overlooked something,
> considering the presence of DNA and my own ligands (e.g., incorrect residue
> names?). An example of the input for AmberMdPrep.sh looks like this:
>
> ./AmberMdPrep.sh -p ATTA_solv.prmtop -c ATTA_solv.inpcrd --mask
> ":25-27&!.H=" --ares "BP1,BP2,CU1" --temp 300 --nprocs 28 --type nucleic
> where BP1, BP2, and CU1 are parts of my organometallic complex, and 25-27
> are their corresponding residues.
>
>
> Thanks !
> –
> Maciej Spiegel, MPharm PhD
> assistant professor
>
> Department of Organic Chemistry and Pharmaceutical Technology,
> Faculty of Pharmacy, Wroclaw Medical University
> Borowska 211A, 50-556 Wroclaw, Poland
>
> Wiadomość napisana przez Daniel Roe via AMBER <amber.ambermd.org> w dniu 18.08.2024, o godz. 00:28:
>
> Hi,
>
> Check the Eval.agr plot of system density vs time and the values in
> Eval.results to make certain everything looks OK, but it’s not unusual for
> systems to be finished within the first final phase. If you check the
> accompanying paper you’ll see that the average time it took for the system
> density to “flatten out” was around 175 ps, so the default value of 1 ns
> was chosen so that most systems would be “done” at that point (only 3 of
> the systems I tested needed longer than that).
>
> So unless something looks weird to you everything might be ok. Let me know
> if I’m not understanding your issue correctly.
>
> -Dan
>
> On Sat, Aug 17, 2024 at 5:03 PM Maciej Spiegel via AMBER <amber.ambermd.org>
> wrote:
>
> Hello everyone,
>
> I found a script written by Daniel R. Roe (
> https://github.com/drroe/AmberMdPrep) that is designed to implement a
> reliable protocol for MD simulations (DOI: 10.1063/5.0013849). I am
> studying the interactions between a B-DNA dodecamer (PDB ID: 1BNA) and a
> metalloorganic complex parameterized by MCPB.py, inserting the complex
> between different DNA pairs. Surprisingly, all the jobs finish in the first
> cycle of the final step, with the .out and .results files similar to the
> example given here: https://justpaste.it/driau .
>
> Could someone kindly confirm whether the jobs have terminated correctly
> according to the script’s requirements? Perhaps I overlooked something,
> considering the presence of DNA and my own ligands (e.g., incorrect residue
> names?). An example of the input for AmberMdPrep.sh looks like this:
>
> ./AmberMdPrep.sh -p ATTA_solv.prmtop -c ATTA_solv.inpcrd --mask
> ":25-27&!.H=" --ares "BP1,BP2,CU1" --temp 300 --nprocs 28 --type nucleic
> where BP1, BP2, and CU1 are parts of my organometallic complex, and 25-27
> are their corresponding residues.
>
> Thanks in advance !
> –
> Maciej Spiegel, MPharm PhD
> assistant professor
>
> Department of Organic Chemistry and Pharmaceutical Technology,
> Faculty of Pharmacy, Wroclaw Medical University
> Borowska 211A, 50-556 Wroclaw, Poland
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>
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Received on Sun Aug 18 2024 - 16:00:02 PDT
