Re: [AMBER] Symmetrical voids during heating stage

From: Thomas Cheatham <>
Date: Thu, 7 Oct 2021 04:22:00 +0000

Goodness, I have to reply again. I did not see the second image with really vacuum slabs (not bubbles). That is unexpected to me. Even with an imaging artifact. Feel free to send inpcrd/prmtop and mdin files (scripts) to me and my lab and we will track down.


p.s. if you look at the box on left and right side you can see the interdigitation where holes on one side are filled on the other, but the other linear gaps inside are not explainable and not the way the water would split in my experience.

One thing to try is in the molecular graphics, show multiple unit cells, likely just an artifact of the visualization. There is not really a gap, since periodically it is fine. Use CPPTRAJ to autoimage the restart. I am now thinking not an artifact. Just a manifest of the environment when you only see one perioidic image, not the entirety. IF I am wrong, hit me up.


\-/ Professor Thomas E. Cheatham, III
-/- Department of Medicinal Chemistry, College of Pharmacy
/-\ Director, Research Computing and CHPC, UIT, U of Utah
/-\ SKH-4914 (801) 587-9652; FAX: (801) 585-6208
\-/ INSCC-410 (801) 585-6318; FAX: (801) 585-5366

From: Nagar, Hemant <>
Sent: Wednesday, October 6, 2021 5:38 PM
Subject: [AMBER] Symmetrical voids during heating stage

Hi All,
I am simulating a dimer protein with water molecules. Initially I am doing restrained energy minimization, after that I am minimizing the energy of whole system. I am heating the system by restraining the protein upto 100 K. When I analyzed my trajectory file of the heating . I am getting voids symmetrical to box dimension. Attached is the image of whole system minimization and heating run. Can anyone help me, Why I am getting those symmetrical voids during the heating stage?
Here are my script files that I am using-
Restrained Minimization
imin=1, maxcyc=10000, ncyc=5000,
ntr=1, ntxo=1, ntb=1,
Group input for restrained atoms
RES 1 482

Whole System Minimization
  maxcyc=6000, ncyc=2000,
  ntb=1, ntr=0,

Heating Stage-
  imin=0, irest=0, ntx=1, ntb=1,
  cut=10.0, ntr=1, ntc=2, ntf=2,
  nstlim=2500, dt=0.002
  ntpr=100, ntwx=100, ntwr=1000
Keep protein fix
RES 1 482

trajin file
trajout heat_V_md1_frames.pdb
#command to run: cpptraj < extract_frames.trajin > heat_V_md1_frames.out

Hemant Nagar

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Received on Wed Oct 06 2021 - 21:30:02 PDT
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