[gmx-users] Regarding wired RDF of TMAO and Aminoacid

[Dilip H N]

1] My simulations in the production MD are for 10 ns. I am first doing
energy minimization, followed by NPT run of 2ns (1000000; 0.002 * 1000000 =
2000 ps[2ns]), and then followed by NPT Production MD run for 10 ns
(10000000; 0.001 * 10000000 = 10000 ps [10 ns]). During the npt simulation,
the box length is reducing, and further during the nptmd ie., production
md too the box length is getting reduced still further. I am not getting
any idea over this... Is the time duration enough or still i need to do it
for more timestep..??

2] Regarding the commands i use to get the mixtures into the simulation box
are:-
(a)  creating the box:- gmx editconf -f abc.gro -o abcbox.gro -c -b X X X
(b)  inserting the molecules:- gmx insert-molecules -f abcbox.gro -ci
def.gro -nmol X -o ghi.gro
(c) Solvating the mixture with water :- gmx solvate -cp ghi.gro -cs
spc216.gro -o jkl.gro -maxsol XXX
So these are the commands which i give in order to generate my Simulation
box containing Amino acid, TMAO and Water mixture.
Hope these are the right set of commands... and then i start
simulation...EM followed by NPT followed by NPTMD...

Thank you...

With Best Regards,

DILIP.H.N
Ph.D Student


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With Best Regards,

DILIP.H.N
Ph.D Student