From: Richard Overstreet (roverst_at_g.clemson.edu)
Date: Wed Jul 22 2015 - 01:05:30 CDT
Abhi,
Are you constraining (fixing) or harmonically restraining the atoms? I
use the following in my config file to fix the graphene monolayer.
fixedAtoms on
fixedAtomsFile <system pdb file>
fixedAtomsCol B
I have also found the graphene can appear to move if the periodic ABC
vectors are not correct.
-Richard
On 07/21/2015 10:59 PM, Abhishek TYAGI wrote:
>
> Hi,
>
>
> I am trying to simulate water and NaCl on top of graphene sheet. While
> performing equilibrium (NVT) I faced following problems:
>
>
> 1. wrapall on
>
>
> The graphene sheet moves to the next grid at the top
>
>
> 2. wrapWater on
>
> wrapAll off
>
>
> The ions moves out of the box
>
>
> The graphene sheet is fixed and restrained. I tried different
> combinations of wrapping during equilibrium run, but still ions are
> moving out of the box.
>
>
> Could you please suggest me, how to solve this.
>
>
>
> Thanks in advance
>
>
> Abhi
>
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