Re: [AMBER] unfolding molecule after heating

From: Ross Walker <>
Date: Thu, 07 Aug 2014 22:33:47 -0700

Hi Annika,

Well that doesn't look good... It's hard to be able to tell what is wrong
though from what you list. I.e. which force field are you using, how did
you build your prmtop and inpcrd file? Are the PBradii set correctly for
IGB=8 etc.

I notice you don't specify a cutoff - this means, I think, that a default
cutoff of 8 angstroms will be used. This is too short for GB runs. You
should set this to something more like 16 or 18 or even 99999 to give you
no cut off. This could be your problem. This will also slow down the
simulations massively. Unless you have a specific reason to be running in
implicit solvent I would suggest trying this in explicit solvent.

All the best

On 8/7/14, 10:16 PM, "Annika Wittenbecher" <>

>Dear amber users,
>I have a problem with my molecule. It's unfolding a lot after 6 stages of
>heating to 300K.
>Here the input file of Stage 6:
>Stage 6 heating of ArsM 250 to
> &cntrl
> imin=0, irest=1,
> nstlim=10000,
> ntc=2,
> ntt=1,
> tempi=250.0,
> ntpr=50, ntwx=50,
> ntb=0,
> /
>Below 3 pictures of 3 different stages:
>Is there anything you can suggest?
>Thank you for your help.
>AMBER mailing list

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Received on Thu Aug 07 2014 - 23:00:02 PDT
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