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
Received on Sun Apr 20 2025 - 15:00:02 PDT
