[gmx-users] potential on non-protein molecules
gianluca.santarossa at unimib.it
Thu May 6 10:04:04 CEST 2004
I just started to simulate non-protein molecules, and I'm dealing
with some unexpected behaviors of my system.
By now, my system consists of an in vacuo simulation of mainly
hydrophobic dendrimers - in this case poli-substituted benzenes bonded
togheter by ammide bonds - in an NVT ensamble usign berendsen
The main problem I have depends on huge fluctuactions of temperature
(10% of the average value of 300K).
The topologies where created using prodrg, then I modified the
parameters using gromacs protein forcefield. The structure consists only
of benzenes and ammide groups, so I think parameters usually found in
proteins should work. What do you think about that?
On the other side, can anyone suggest me an hydrophobic solvent I can
use, so I can try an explicit solvent simulation?
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