[gmx-users] request

[Dinesh Pinisetty]

Hi all,
         I am able to run the simulations,I want to figure out diffusive
property.
          I ran the practice simulations given in GROMACS tutor.I have run
for the mixture of methanol and water there I was able to figure out the
diffusive property by calling g_msd.There I got options as system,MeOH and
water its giving diffusivity values differently,If D value of MeOH was
given I assumed that its the value of methanol diffusivity in
water,similarly for water I thought its the diffusivity of water in
methanol,but I did not get what the diffusivity of the system mean,is it
the self diffusivity value of the mixture or anything?
    I have run the simulation for DMPC how to figure out the diffusive
property of water through DMPC as such or self diffusivity of the
DMPC+water etc.If I am calling g_msd subroutine its showing the error as
FATAL error: topo1.tpr does not exist or so.
How to modify topo1.tpr file to fullmd.tpr or input .tpr etc and how to
figure out the diffusivity of the membranes in water etc.
Someone please let me know this as soon as you see this query.
Thanks a lot in advance,for help in this regard.

Thank you,
Dinesh.