[gmx-users] Re: The molecule size (jiqing)

[Mark Abraham]

主月 ：） wrote:
> Hi:

> Two things,
> 
> - maybe you need a larger systems
> - maybe g_gyrate does not take periodicity into account correctly.
> extract some single molecules and look at them in a viewer, or write
> your own script to compute Rg.
> - have you used pbc = full for the simulations?
>  
> 1.*The cell length about my PVME model is 4.5 nm which is big enough for 
> a PVME chain possesses all trans conformation.*

Fine, that would be a minimum necessary condition for something that was
expected to extend fully. You should actually increase that so that in
such a case the opposite ends can't see each other. You need margins at
least as large as your largest cut-offs. You can see if this is a
potential problem by seeing if any of your monomers do extend in this
way. Your experimental system probably had room for about 10^8 such
chains end to end, so there is a chance you're comparing apples and
oranges here.

> *2. The Rg is anaylzed by my own program, which has been validated.*
> ** 
> *3.PBC=XYZ*

Has this force field been demonstrated to be effective for this sort of
simulation? If not, maybe you've begun to demonstrate that it isn't?

Mark