[AMBER] Solvent Box Issue When Running AMBER Dynamics

From: Zhang, Sixue <szhang74.illinois.edu>
Date: Wed, 4 Mar 2015 22:46:37 +0000


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.

Thanks a lot,

Sixue Zhang

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Received on Wed Mar 04 2015 - 15:00:02 PST
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