Re: [AMBER] [Sender Not Verified] Re: AMBER error vlimit exceed for step

From: He, Amy via AMBER <amber.ambermd.org>
Date: Wed, 20 Mar 2024 19:21:02 +0000

Hi Vero,

Not sure this helps, but besides energies, have you looked at other physical properties, such as temperature and density, in the steps before you encountered the vlimit exceed error?

What other types of simulations did you run between minimization and the restraint-free (?) NPT equilibrium, and how did they go?

If you can’t post on the list server, having someone you trust or within your institution to look at details of your simulations might help. 

--
Amy He
Hadad Lab . OSU
He.1768.osu.edu
From: VERONICA MARTIN HERNANDEZ via AMBER <amber.ambermd.org>
Date: Wednesday, March 20, 2024 at 2:07 PM
To: David A Case <dacase1.gmail.com>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] [Sender Not Verified] Re: AMBER error vlimit exceed for step
Hi
Thanks for the advice. I have performed the autoimage command, and I see how the system blows up
I have also put the input of nstlim=0 but I've got an error and the calculation doesn't start, there is an error mcbarint. Due to that  error, I have tried to put nstlim=200, and save every step and there is a point where the temperature increases like 10000 K
So, now, I don't know what is happening in my system
Thanks for all the help and I hope I have explained it well
Best regards
Vero
________________________________
De: David A Case <dacase1.gmail.com>
Enviado: miércoles, 20 de marzo de 2024 15:29
Para: VERONICA MARTIN HERNANDEZ <veronica.martin.hernandez.uva.es>; AMBER Mailing List <amber.ambermd.org>
Asunto: Re: [AMBER] [Sender Not Verified] Re: AMBER error vlimit exceed for step
On Mon, Mar 18, 2024, VERONICA MARTIN HERNANDEZ via AMBER wrote:
>
>Thanks for the advice, I am seeing the problem: the water box
>desintegrates, it's like a water leak in a glass.
Have you run the cpptraj "autoimage" command before doing the visualization?
What you describe sounds like a common problem.
I am still not sure why you seem to be unwilling to set nstlim=0, and then
to examine carefully the energy output from the initial step, comparing it
to the final step of minimization.
...hope this helps....dac
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Received on Wed Mar 20 2024 - 12:30:02 PDT
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