[gmx-users] Unable to maintain proper density of polyunsaturated fatty acid

Tushar Ranjan Moharana tusharranjanmoharana at gmail.com
Thu Mar 5 20:27:03 CET 2015


Hi everyone,
I am trying to make a bi-phasic system of water and triglyceride of poly
unsaturated fatty acid. While making a box full of triglyceride of poly
unsaturated fatty acid I encounter following problem.
insert-molecule placed 126 molecule in 10nm *10nm*10nm cube. To get
expected density around 500 molecule should be placed. I tried to do energy
minimization followed by solvate the box with triglyceride but it did not
work.
During energy minimization of the above system E pot. remains positive
(order of 10^4) and in later during *nVT* simulation all the molecule goes
out of the box. When *nPT* simulation was done at 2 bar an error message
come saying some molecules moved during simulation.
I am using CHARM36 all atom force field and topology (.itp) file was
created by swiss param. I simulated a single molecule in a box of
3nm*3nm*3nm. Everything went fine even though E pot after energy
minimization was positive (order of 10^2) in this case too.

Any suggestion to try is most welcome.

Thanks for your time and effort.

-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB


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