Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics

From: Zhang, Sixue <>
Date: Mon, 9 Mar 2015 20:58:53 +0000


Thank you for all your helps. I solved my solvent box issue. It was actual bubbles caused by a sudden heat up, not wrapping problem. After I changed my heating procedure to a smoother one, I am able to eliminate those bubbles in NVT now.



-----Original Message-----
From: Daniel Roe []
Sent: 201539 9:59
To: AMBER Mailing List
Subject: Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics


You still have the same issue as before - your system's density is way, way too low in both restart files (~0.85 g/mL). You need to allow your system's density (i.e. box dimensions) to properly relax.
According to your output you ran 100 ps in NTV ensemble - this will
*not* get you an equilibrated system and in fact is what is letting those vacuum bubbles form in your simulation. You can run a short (<
15 ps) initial relaxation of solvent in NTV (holding solute fixed), but afterwards you're going to have to run in NTP to let your density equilibrate. If you're interested, I've previously posted the protocol I tend to use on the list, which you can view here:

Note of course this is by no means the only way to do it. However, whatever procedure you use to equilibrate, you need to make certain that your system's density and energy values look reasonable before considering running production dynamics.

Hope this helps,


On Wed, Mar 4, 2015 at 3:46 PM, Zhang, Sixue <> wrote:
> Hello,
> I brought out an solvent box issue to this mailing list a few weeks ago. I found that the solvent box became very weird in shape after dynamics (NVT or NPT). It looks like the water was boiling. I was not sure whether it was a wrapping problem or improper equilibration. I then did more tests according to people's suggestions. One Post-doc in my group who is very experienced in AMBER built and equilibrated my system from scratch. She also ended up with this bad box shape. She is pretty sure she equilibrated it properly. In one of my new test, I put high restraints on all atoms, 200 kcal/mol, which means everything almost can't move. If there is no wrapping problem, the solvent box should stay at the same shape after NVT. However, I found some part of the solvents still gradually evolved to a bad shape while the rest part stayed at their original positions as expected. Does anybody has any idea about this issue or has some suggestion on wrapping the system?
> Below is the dropbox links for one set of my test files in case you would like to take a look.
> l=0
> Thanks a lot,
> Sixue Zhang
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)

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Received on Mon Mar 09 2015 - 14:30:02 PDT
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