Cut offs.



 Hi,
 To my knowledge there are not many studies of how to treat cutoffs in
 the literature. However in Proteins: Struct. Funct. Genet. 6:32-45 (1989)
 there is a quite extensive study. They have used the CHARMM force field,
 however I think this may account for any similar force field.
 My opinion is that the cutoffs that one has to use is very dependent on
 how the electrostatics of the calculation is treated.
 I'm a Sybyl User that use the AMBER FF in Sybyl for dynamics and
 mechanics calculation of biomolecules. For vacuum calculations I use a
 cutoff of 10-12 A (distance dependent dielectric constant) and 8-10 A
 for solvent calculations.
 The effect of the cutoffs to the vdW forces is less important I think.
 These long range vdW forces does not have any large impact on the
 structure, but may of course change the total energy level of a
 calculation.
 Finally, I think that what may become even more important is to include
 polarizability to the electrostatics, especially for biomolecules. Not
 before that becomes real we will treat simulations of biomolecules in
 the best possible way. I have heard from a colleague about a new structure
 of an ion transporting protein which had a narrow channel where in one the
 sides of this channel it was up to 5-7 lysines or arginines and the other
 side contained about 4 aspartates or glutamates. These residues were
 clustered very near eachother. Would anybody think that a molecular
 dynamics simulation of this protein would be succesful using todays
 standard force fields ? I hesitate......
 Any comments to the net regarding these questions would be very much
 welcomed by me, because I think it is very important for the improvement
 of the MD techniques in biological chemistry (which I think and hope is
 and will be a very useful tool).
 Greetings
 Martin Norin
 KTH
 Stockholm             e-mail:martin "at@at" physchem.kth.se