Re: [AMBER] Conformation of NEB end states changing during 1HEAT

From: Ghoreishi, Delaram <>
Date: Mon, 18 Nov 2019 17:29:36 +0000

Hi Madhur,

Can you send me your prmtop and coordinate files? I can look into it and see if I can reproduce your result.


From: Madhur Aggarwal <>
Sent: Monday, November 18, 2019 12:09 PM
Subject: [AMBER] Conformation of NEB end states changing during 1HEAT

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Hi all,

I am using Amber18 to run NEB simulations on my protein + water system. I minimized both the end states and made sure the prmtop file generated is the same for both the end states. Then, I am following Tutorial A5 on NEB calcs on Alanine dipeptide.
The issue is when I run step 4 to generate images and heat the system, my end states are also undergoing a change in their conformation, which should not happen (attached
When I try doing the calculations on Alanine dipeptide in implicit solvent (as done in the tutorial), it works fine. So, I thought maybe it has something to do with my explicit solvent. But when I do the calculations on my system using implicit solvent, the conformations of my end states are still changing (attached
I am not able to figure out why this is happening. I would really appreciate if someone could help me out with this. I have attached my input scripts for both implicit and explicit solvent cases here.

Madhur Aggarwal

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Received on Mon Nov 18 2019 - 09:30:03 PST
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