Re: [AMBER] unfolding molecule after heating

From: Ross Walker <>
Date: Thu, 07 Aug 2014 22:35:15 -0700

Ah - now I look again I do see the cutoff specified so that's not the
problem assuming you had it set like that at all stages.

I'd still consider trying this in explicit solvent to see how it goes.

Beyond that we'd need a lot more info about how you setup this system.

All the best

On 8/7/14, 10:33 PM, "Ross Walker" <> wrote:

>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 - 23:00:03 PDT
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