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

From: Carlos Simmerling <>
Date: Mon, 18 Nov 2019 12:40:13 -0500

I'm a little confused about what's happening. you say that alanine
dipeptide works fine in implicit solvent, but your system does not work
fine in implicit solvent? if so, then for now let's ignore explicit solvent
since you have 2 setups to compare, and one works while the other does not.
did you compare line by line the input file for your system vs the one you
used for the dipeptide that worked? you didn't include the working example
here so we can't test that. you also want to compare the run scripts, not
just the mdin files. something must not be the same.
it can also help to carefully look at the mdout files and make sure it is
doing what you think it should. again, you have a working example and a
non-working example, so you can compare them.

On Mon, Nov 18, 2019 at 12:10 PM Madhur Aggarwal <> wrote:

> 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.
> Thanks,
> Madhur Aggarwal
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Received on Mon Nov 18 2019 - 10:00:02 PST
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