[gmx-users] system is exploding

taveechai taveecharoenkool taweehui at yahoo.com
Mon Sep 12 18:46:21 CEST 2005

dear all,
 thanks itamar. but i already tried what you suggest.
i 'd like to put my question again.
 >  i have system contains proteins in hydrated popc
> bilayers. these proteins have a pore in the middle.
> put one ion in the middle of the pore and then run
> but at the step around 10,000 there are warning "
> system is exploding".  However, i ran this system
> (without ion) in 5ns and it doesn't have warnings.

maybe i have to clarify my question. 
 1. i want to study free energy of K in this pore
between having +1 charge and 0 charge...how to do.
This sytem(proteins in hydrated bilayer) is
equilibrated for 5 ns. i have tried to calculate free
energy by changing lamda from 0 charge to +1.... i got
some values... but when i looked at the K ion in the
pore ...K ion went into the lipid bilayers .. maybe
because it has 0 charge but i think it shoudn't have
the reliable result. Because positive charge in the
lipid sounds strange. 
 2. i put K ion in the pore (middle of the pore) ,
perform energy minimization, but after looking the
picture from rasmol,  proteins went to the corners and
water came in the middle of bilayers(i mean it still
looks like bilyers but water in the middle) . do u
know why?
 3. i remove water that in the position of K  in the
pore and then perform energy minimization the system
still looks like in no.2
 4. i don't exactly understand 'system is exploding' .
does it mean Lincs cannot move atoms to constraint
value. because i look at the picture after system is
exploding with rasmol the system look normal. i expect
molecules of lipid to disperse in the box
 5. if someone know how to calculate free energy
rapidly please mail me
thank you

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