[gmx-users] dppc+mixture

Xavier Periole x.periole at chem.rug.nl
Fri Oct 29 10:31:39 CEST 2004

Dinesh Pinisetty wrote:

>Hello all,
>          I have taken a mixture of water and methanol,methanol being very
>less only around 10% of water molecules(2711 water molecules and 300
>methanol molecules).
>          I have placed this box with mixture on either side of DPPC 48/48
>bilayer.When I performed Energy minimization,all the methanol molecules in
>the bottom box escapes into the box which is above i.e on the other side of
>the bilayer.Why is this happening is it due to periodic boundary
>conditions? but when I checked the minimization(i.e when I have loaded .gro
>file in VMD and viewed m.trr file it looks that some methanol molecules are
>present in the bottom box) but again when I view the .gro file created
>after minimization I cannot see any methanol molecules,can this happen? but
>why methanol molecules are moving from bottom box to the above box.
>Thanking you,
>Yours sincerely,
Seeing molecules moving during minimisation is a bit unusual !!! You 
should check the
box dimensions, it might be the problem ...



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

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