[gmx-users] [SPAM]: Re: Coarse Grained (Empty space In water)

[Justin Lemkul]

On 6/4/18 1:20 PM, Samieegohar, Mohammadreza wrote:
> Hi Kevin
>
> The nanoparticle is fixed in the middle of box and is not in the edge.
>
> I used PBC boundary condition
>
> Is it because of water freezing ?

Voids observed during NVT are generally due to setting up an initial box 
that is too large for the given number of particles. NPT equilibration 
should compress the system.

-Justin

>
>
>
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kevin Boyd <kevin.boyd at uconn.edu>
> Sent: Monday, June 4, 2018 12:58:13 PM
> To: gmx-users at gromacs.org
> Subject: [SPAM]: Re: [gmx-users] Coarse Grained (Empty space In water)
>
> Hi,
>
> Why would you want to "ruin" a perfectly good nanoparticle? :)
>
> Could this be a visualization artifact? What kind of treatment of
> periodic boundary conditions are you applying prior to visualization?
> If you use a PBC option that makes your nanoparticle  contiguous and
> not split across periodic boundaries, you would see an empty area in
> the box if the nanoparticle is partially out of the box (which would
> correspond in size to the fraction of the nanoparticle out of the
> box).
>
> Kevin
>
> On Mon, Jun 4, 2018 at 12:48 PM, Samieegohar, Mohammadreza
> <mohammadreza.samiee at howard.edu> wrote:
>> Hello
>> I am ruining a nanoparticle inside water. I use coarse grained model for water and nanoparticle
>> My problem is:
>> When I run the system in NVT 298K , after some steps there is a empty area inside the water  (like a hole) while the initial structure has a good distribution for water molecules (P4).
>>
>> May you help me to solve the problem ?
>>
>> Thanks
>>
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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