[gmx-users] Periodicity in x-y plane (Neda Rafiee)

Björn Sommer bjoern at CELLmicrocosmos.org
Mon Feb 6 12:32:15 CET 2017

Hi Neda,

On 6/02/2017 8:43 am, gromacs.org_gmx-users-request at maillist.sys.kth.se
>    6. Periodicity in x-y plane (Neda Rafiee)
> Message: 6
> Date: Mon, 6 Feb 2017 11:08:42 +0330 (IRST)
> From: Neda Rafiee <nerafiee at ipm.ir>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Periodicity in x-y plane
> Message-ID: <12473704.8815.1486366722721.JavaMail.root at zmail.ipm.ir>
> Content-Type: text/plain; charset=utf-8
> Hi. I have already built a lipid bilayer and I want to create a box for it and fill it with water. I used : 
> $ gmx editconf -f renumber.gro -o newbox.gro  -c -box 8 8 14 -bt triclinic  
> and after that I used:
> $ gmx solvate -cp newbox.gro -cs tip4p.gro -o solvated.gro -p topol.top  
> but when I see solvated.gro in VMD, in periodicity , I check x +x or y +y direction, I see man water molecules between adjacent neighbors in x-y direction and it destroy the periodicity of my membrane in x-y plane, while I want to have water only in the upper and lower sides of the membrane. What should I do? 
Please play around with this:

Shortly, in VMD use in the Graphical Representations window a selection like
not ((resname 'W' 'NA+') and within 5.5 of (not resname 'W' 'NA+'))

See the previous link for more info. Basically, make sure that no water
is inside the membrane but also that the distance between the water bath
and the head groups is not too small, otherwise the box will shrink
during simulation and the membrane might deform a little bit.

After that, use the regular PDB export and make sure to select the
actual selection in the export window!/
Have fun!

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