normal Postional restraints on lipids

  • daver
  • daver's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
12 years 10 months ago #670 by daver
Postional restraints on lipids was created by daver
Hi,
I've run across a problem I can't sort out. I've built a system of 128 POPC molecules and 820 waters that I think have been successfully mapped into a CG system. They sucessfully minimized but when I try running them in a semiisotropic MD run I always get a membrane collapse. I thought that maybe running with positional restraints on the Z axis might help, but I can't figure out how to set this up in the topology file. I've got:
#include "martini_v2.1.itp"
#include "martini_v2.0_lipids.itp"
and always get errors with the restraints in the wrong place.
-david

Please Log in or Create an account to join the conversation.

More
12 years 10 months ago #671 by xavier
Replied by xavier on topic Postional restraints on lipids

daver wrote: Hi,
I've run across a problem I can't sort out. I've built a system of 128 POPC molecules and 820 waters that I think have been successfully mapped into a CG system. They sucessfully minimized but when I try running them in a semiisotropic MD run I always get a membrane collapse. I thought that maybe running with positional restraints on the Z axis might help, but I can't figure out how to set this up in the topology file. I've got:
#include "martini_v2.1.itp"
#include "martini_v2.0_lipids.itp"
and always get errors with the restraints in the wrong place.
-david

The system should be fine without restrains ... you should check all your input files starting by the mdp file .. the gro file and look at what could cause the collapse.

Please Log in or Create an account to join the conversation.

Time to create page: 0.081 seconds