I think if you want any relevant advice you'll need to be a lot more
specific about what you're trying to do, how you built the systems, and how
the standard md turned out.
On Mon, Apr 21, 2025, 5:45 PM VERONICA MARTIN HERNANDEZ via AMBER <
amber.ambermd.org> wrote:
> thank you all for the answers
>
> I have tried all the solutions you provided, but the bubbles persist. I
> tried the tutorial, running first NPT and then NVT....nothing works. I
> think is due to the small size of the box (I only solvated the ligands of
> the H-REX) and the use of GPUs. The only thing that seems to solve the
> problem is running the minimization in CPUs.
>
> I really appreciate all the help, and thanks in advance
>
> Vero
> ________________________________
> De: Daniel Roe via AMBER <amber.ambermd.org>
> Enviado: lunes, 21 de abril de 2025 17:35
> Para: AMBER Mailing List <amber.ambermd.org>
> Asunto: Re: [AMBER] H-REX and bubles
>
> In addition to what Adrian suggested, you may want to try this script
> (and check the associated publication) which attempts to automate and
> simplify the process of relaxing an explicitly solvated system:
>
> https://github.com/drroe/AmberMdPrep
>
> -Dan
>
> On Sun, Apr 20, 2025 at 5:47 PM Adrian Roitberg via AMBER
> <amber.ambermd.org> wrote:
> >
> > Hi Veronica
> >
> > You need to follow some stricter protocols, such as the one here:
> > https://ambermd.org/tutorials/basic/tutorial13/index.php
> >
> > Bottomline, at some point you MUST do NPT to get rid of your bubble.
> >
> > Adrian
> >
> >
> > On 4/18/25 2:49 PM, VERONICA MARTIN HERNANDEZ via AMBER wrote:
> > > [External Email]
> > >
> > > I have performed stable MD before, but my question is: under H-REX the
> relaxation step should be performed at each lambda value or maybe just an
> NPT relaxation and then NVT equilibration at one lambda value??
> > >
> > >
> > > Just I don't know which could be better
> > >
> > > Enviado desde Outlook para Android<https://aka.ms/AAb9ysg>
> > > ________________________________
> > > From: Carlos Simmerling <carlos.simmerling.stonybrook.edu>
> > > Sent: Friday, April 18, 2025 2:48:04 PM
> > > To: VERONICA MARTIN HERNANDEZ <veronica.martin.hernandez.uva.es>
> > > Cc: Carlos Simmerling <carlos.simmerling.stonybrook.edu>; AMBER
> Mailing List <amber.ambermd.org>
> > > Subject: Re: [AMBER] H-REX and bubles
> > >
> > > I suggest starting with the introductory tutorials on the Amber page.
> Make sure that you can carry out stable standard MD before moving on to any
> advanced methodsm
> > >
> > > On Fri, Apr 18, 2025, 8:28 AM VERONICA MARTIN HERNANDEZ <
> veronica.martin.hernandez.uva.es<mailto:veronica.martin.hernandez.uva.es>>
> wrote:
> > > I have tried to increase the equilibration steps, but I don't know if
> i should try to perform the equilibration at CPUs or maybe perform NPT
> equilibration instead of NVT....
> > > I don't know
> > >
> > > Enviado desde Outlook para Android<https://aka.ms/AAb9ysg>
> > > ________________________________
> > > From: Carlos Simmerling <carlos.simmerling.stonybrook.edu<mailto:
> carlos.simmerling.stonybrook.edu>>
> > > Sent: Friday, April 18, 2025 2:15:01 PM
> > > To: VERONICA MARTIN HERNANDEZ <veronica.martin.hernandez.uva.es
> <mailto:veronica.martin.hernandez.uva.es>>; AMBER Mailing List <
> amber.ambermd.org<mailto:amber.ambermd.org>>
> > > Subject: Re: [AMBER] H-REX and bubles
> > >
> > > H-REX? if this is replica exchange, then you probably want to make
> sure all of your systems are properly relaxed before using them as inputs.
> so I wouldn't focus on the H-REX part, but instead go back to your building
> and relaxation protocol and find out why it did not properly relax the
> volume/density. there are tutorials for this on the Amber home page.
> > > for more detailed help we would need to know exactly what you did for
> these steps.
> > >
> > > On Fri, Apr 18, 2025 at 8:12 AM VERONICA MARTIN HERNANDEZ via AMBER <
> amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
> > > Hi, I'm performing at H-REX with a system all in GPUS, but, in the
> first step of the equilibration, there is a bubble and I don't know how to
> fix it
> > >
> > > Could anyone help me?? I think that maybe performing a little NPT
> equilibration and then a NVT equilibration could fix this issue, but I
> don't now
> > >
> > > Thanks in advance
> > >
> > > Vero
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > --
> > Dr. Adrian E. Roitberg
> > Frank E. Harris Professor
> > Department of Chemistry
> > University of Florida
> > roitberg.ufl.edu
> > 352-392-6972
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Apr 21 2025 - 16:00:02 PDT
