[gmx-users] Re: 1-4 interactions free energy calculations

Sonia Aguilera sm.aguilera37 at uniandes.edu.co
Tue Jun 25 22:36:35 CEST 2013

Hi Justin, 

Thank you for your answer. I’m performing several tests to see what is the
best for my system. The reason I decided not to couple the intramolecular
interactions is because I think that the annihilation of the molecule will
lead to very extreme configurations and that will affect my phase-space
overlap. I know I can just increase the number of intermediate states, but I
wanted to first test my theory. Also, I have limited resources to run. 

There is a gap between the indirect and direct calculation methods  for my
system. If I set up couple-intramol=no, then I can´t use domain
decomposition but particle decomposition in all simulations (charge groups
are too big, and there is no domain decomposition… ) and I got the 1-4
interactions warning. If I restrain the h-bonds, then the minimization
converges but not to Fmax less than 100 in only 499 steps and 12 minutes (8
cores machines). If I continue and run the NVT stabilization, then it takes
17h20min to complete only 100 ps, and I still got the 1-4 interactions
warning. I still have to run the NPT and 3 ns MD, which will take too much
time. I think it worth it  because I think it will help with the phase-space
overlap, and I will only have to perform 20 series of simulations (vdw and
coulomb separately) to get the free energy change. 

On the other hand, if I set up couple-intramol=yes, then I have to run 20
extra simulations in vacuo to counter the annihilation effect. I think that
it will also affect the phase-space overlap. The good thing is that I can
use domain decomposition and the minimization converges to machine precision
(takes 7000 steps and around 40 minutes in a machine with the same
characteristics that the previous one). Also, the same 100-ps NVT takes only
3h20min. If I think of the overall picture, it seems that the total time I
will spend doing dd (coupleintramol=yes) rather than pd (coupleintramol=no)
will be less. However I’m worried about the phase-space overlap and the
available resources I have for running since it makes difficult to just
increase the intermediate states.

Also, I think I can try doing the same but with the 4.6.1 version. It looks
like I can now couple both vdw and coulomb in the same simulation
I have also wanted to try expanded ensemble to improve my sampling, but I
have not found that much documentation about the implementation on gromacs.
It would be great if you can provide an example. 

So, do you know another way to improve my sampling and the phase-space
overlap that can help me to solve my problem?  Also, I’m working with a
charged molecule. Would it help in any aspect if I neutralize the system?
Thank you very much in advance, 

Best regards,

Sonia Aguilera
Graduate Assistant
Department of Chemical Engineering
Universidad de los Andes

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