[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

J B john.b.86 at hotmail.com
Sun Apr 29 10:46:31 CEST 2012

> Is the problem specific to cylinder geometry?  Do other settings work?  Does it 
> make a difference if you set values for pull_r0 and pull_r1?
> -Justin

I would think that it is the cylinder geometry that creates the problem.
If I use 
pull            	= umbrellapull_geometry   	= distancepull_dim        	= N N Ypull_start      	= yespull_init1		= 0.0pull_ngroups    	= 1pull_group0     	= DPPCpull_group1     	= drugpull_rate1      	= 0.0
The molecules stays in place. But pull_geometry=distance is what I would prefer due to the undulations.
Changing pull_r0 and pull_r1 still makes the drug molecule move down towards the membrane... 		 	   		  
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