[gmx-users] question on KALP-15 in DPPC tutorial

[Mark Abraham]

On 21/11/2010 8:45 PM, Amit Choubey wrote:
> Hi all,
>
> I was going through the very nicely presented tutorial by Justin (on 
> KALP-15 in DPPC). I have one question regarding the non-bonded 
> cut-offs. It seems that people use many different values of non-bonded 
> cut-off (varying from 0.9 nm to 1.2 nm or probably more). How should i 
> choose the cut-off values for my simulations ?

In the first instance, by reproducing the conditions under which the 
parameters were validated. Unfortunately, most of the force fields were 
not parametrized for PME, under which they are often now used. So look 
at some papers from large well-known groups that have done something 
similar to what you want to do, judge how well they have worked, and do 
something comparable. Unfortunately, there have been little or no 
systematic studies of how accurate forcefield X plus PME needs to be to 
model reality usefully. Hopefully that will change :-)

Mark