Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber

From: Charo del Genio <>
Date: Wed, 26 Aug 2020 14:57:38 +0100

On 26/08/2020 14:07, Matias Machado wrote:
> Dear Charo,
> Thanks to David and Scott's help we advanced a lot in debugging the issue...
> This problem only shows up in cmake builds of AMBER Tools, while legacy builds work just fine...
> Scott was observing the same odd things you are pointing in the code.
> I did some tests and in fact comment lines stating with '#' are the only ones generating the buffer overflow.
> This bug is not only restricted to SIRAH as the same issue will happen in AMBER ports of CUFIX.
> On the other hand, comments after the parameter definition are not giving any problem, as they don't in other AMBER files.
> Some fixes have been committed at both AMBER and SIRAH sides.
> Best,
> Matías
> PS: While ago, I sent to the mailing list a reference topology based on Tutorial 5 as a control to check the correct loading of LJoff.frcmod. But I guess it got stuck awaiting for a moderator due to the file size :-(

Dear Matias,
        I checked the 1CRN example/reference, and removing the comments as I did before produces a prmtop file that is identical to the one you sent. I guess this confirms the whole discussion.

However, this also seems to suggest that the instabilities I'm observing are due to something else. Up to when I wrote to the mailing list, I was following more or less the example protocols given on
the SIRAH web site. So, after minimizing the system, I went directly for an equilibration at the final temperature (22 °C) at constant pressure. Normally, I would have first heated the system at
constant volume over some period of time starting from 0 K, and then switched to constant pressure. Do you reckon this may remove the instabilities? (In fact, I may just try and check).

Or maybe should I try to equilibrate the system even more gently? Note that the main problem seems to be due to the waters, because if I impose extreme restraints (500 kcal/mol Ų) on every atom
except the solvent, still vlimit is exceeded from step 2. Again, this only happens if I use the Bussi (v-rescaling) thermostat, or Langevin with a more common gamma_ln such as 2; using Langevin with
gamma_ln=50 stabilizes the system.



Dr. Charo I. del Genio
Senior Lecturer in Statistical Physics
Applied Mathematics Research Centre (AMRC)
Design Hub
Coventry University Technology Park
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Received on Wed Aug 26 2020 - 07:00:03 PDT
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