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
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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
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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
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Received on Fri Apr 18 2025 - 12:00:02 PDT
