[gmx-users] regarding rdf

[Neha Gupta]

Hi,

I take the following steps to perform rdf calculation for my organic
molecule.

min, min2, eql, eql2 and prd.

In order to check, whether my molecule is intact, I generate .pdb of the
entire system after each step.

Till eql step, my molecule remains intact.

After eql2, the molecule breaks.


I make use of the following code for eql :

integrator               = md
dt                       = 0.002     ; 2 fs
nsteps                   = 500000    ; 1.0 ns

nstenergy                = 200
nstlog                   = 2000
nstxout-compressed       = 10000

continuation             = yes
constraint-algorithm     = lincs
constraints              = h-bonds

cutoff-scheme            = Verlet

coulombtype              = PME
rcoulomb                 = 1.0

vdwtype                  = Cut-off
rvdw                     = 1.0
DispCorr                 = EnerPres

tcoupl                   = Nose-Hoover
tc-grps                  = LIG      Water
tau-t                    = 2.0       2.0
ref-t                    = 298.15   298.15
nhchainlength            = 1

pcoupl                   = Parrinello-Rahman
tau_p                    = 2.0
compressibility          = 4.46e-5
ref_p                    = 1.0


How to fix it?

Thanks,
Neha