- Posts: 1
Postional restraints on lipids
- daver
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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
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
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- xavier
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12 years 10 months ago #671
by xavier
Replied by xavier on topic Postional restraints on lipids
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.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
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