AW: Restart simulation of an equilibrated bilayer with sugar molecules inserted

From: Norman Geist (
Date: Mon Mar 18 2013 - 01:39:50 CDT

Hi Keller,


I’m not sure if I stand alone with this opinion, but you will have to build
a new simulation box and run a new, but maybe shorter, equilibration, as the
bilayer represents its equilibration state already due its updated
coordinates. I think it’s not a good idea, or not worth it, to edit the
restart files to remove water and add sugar molecules. This will destroy the
pressure equilibrium anyway and additionally, how would you assign
velocities to the the sugars? This would furthermore destroy the
temperature, won’t it? As you already equilibrated your bilayer, it
shouldn’t take too much time to re-equilibrate it in the new environment.


If you are really sure, that you want to do this, you should start adding
the sugars to a pdb of you system (copy the pdb lines). Remember the water
atoms you remove (I guess you will have to). Generate a new psf file (like
you always do). Edit the vel file (pdb format) to remove the waters
mentioned above and to add the sugars. I guess it’s better not to assign
any velocitities to the sugars and better do it with a short temperature
controlled run (but not temperature reassigning or rescaling). This should
be it. But really, the time you will need to place the sugars within the
solvent, will take more time than re-equilibrating the system ;)


Good luck.


Norman Geist.


Von: [] Im Auftrag
von Keller Wenger
Gesendet: Sonntag, 17. März 2013 15:51
Betreff: namd-l: Restart simulation of an equilibrated bilayer with sugar
molecules inserted


Hi, everyone,


I have got a fully equilibrated DPPC bilayer system. I have .pdb, .psf,
.coor, .vel, and .xsc files able to restart the simulation for the DPPC
system. Now I need to insert several sugar molecules into water layers above
and below the bilayer. But I only have .pdb and .psf files for these sugar
molecules. So, how can I restart simulating such a combined system without
destroying the equlibrated DPPC system? Since it is only a minor change to
the whole bilayer system, I think I don't need to re-equilibrate the
integrated system from a scratch.


I can generate integrated .pdb and .psf files for DPPC+sugar, but I have no
idea how to generate integrated .coor, .vel and .xsc files.


Any suggestions would be really appreciated.



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