[gmx-users] Insert Gold nanoparticles in a simulation box

[Dallas Warren]

Simply copy/paste the text from the coordinate file for the nano
particle onto the end of the coordinate file for the monolayer.  Of
course, you need to only insert the coordinate lines, not the text at
the start (description and number of atoms in a .gro file) or end (box
dimensions in a .gro file), and adjust the number of atoms (line 2 in
a .gro file)
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 16 June 2017 at 22:21, Sheikh Imamul Hossain <s.imamul.ku at gmail.com> wrote:
> Hi all,
>
> I am simulating CG lipid monolayer in a pbc box of dimension 22*22*50 nm3.
> Now I want to introduce 5/6 CG gold nanoparticles 3/4 nm above the
> monolayer in my system. For this purpose I have edited the box dimension to
> 22*22*4 nm3 and translated 3/4 nm above the monolayer to insert the CG gold
> nanoparticles in that box. But when I use the command *gmx insert-molecules
> -f monolayer.gro -ci gold.gro -o gold_monolayer.gro -nmol 5* then it does
> not add any CG gold molecules in the box. Surprisingly the same command
> works to add 5 CG gold molecules randomly in the free space when the box
> size is considered 22*22*50 nm3.
>
> How can I solve this problem?
>
> Thanks in advance.
>
> Sincerely Your’s
> *Sheikh Imamul Hossain*
> PhD Research Student
>
> Queensland University of Technology
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