[AMBER] Heating the soft core atoms in TI simulations

From: He, Amy via AMBER <amber.ambermd.org>
Date: Wed, 25 Jan 2023 01:01:20 +0000

Dear Amber Experts,

I have a question about Amber TI simulations with soft core potential.

I want to do a single step morphing and calculate the energy difference of changing the charge states of two residues in a protein.

My system is solvated with explicit waters. There are three soft core atoms: The appearing/disappearing H, and two nearby atoms that have different types in different charge states. SHAKE is applied to all hydrogens except the residues containing these soft core atoms.

To set up an equilibrated initial structure for the production TI simulations, I was trying to minimize, heat and press the initial and the end states.

After running a 50-ps(25000*0.002) heating step: From my MD output, I found that the soft core atoms did not achieve a stable temperature of 310K.

Is it normal for soft core, non-SHAKE atoms to not achieve a stable temperature? Or is it because we are calculating the temperature for only 3 atoms? Or is there anything I did wrong? :(

Also, is there an upper limit for the number of soft core atoms? Does it make more sense to include the whole residue? Will that drastically increase the computing cost?

Any suggestion would be greatly appreciated. I look forward to learning more about TI simulations.

Many Thanks,

Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
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Received on Tue Jan 24 2023 - 17:30:02 PST
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