[gmx-users] Problem calculating RMSD with gromos

Melchor S. msmqbm at cid.csic.es
Tue Jul 2 14:45:45 CEST 2013

Hi all,

I am trying to calculate an RMSD of two simulations. All the setting are
equal for both, but  i use OPLS in one and for the other gromos53a6.

I wanted to calculate the RMSD between the trajectory and the
crystallographic structures(Open and closed forms). The simulation involves
a protein that starting from a closed conformation, opens the active center
after some ns.  So I expect a very small RMSD at the beginning , that then
will increase, compared to the closed form, and when I calculate the RMSD,
respect to the open form, the opposite.

With OPLS both using VMD and g_rms, I obtain the expected RMSD ( I run two
simulations with succes), but with Gromos96 53a6 no. I have made three
different simulations with gromos53a6, changing the initial velocities, but
I don't have any succes. I don't know what could be the reason, some of you
have had this problem previously? Any solution a part of try with another

Thanks in advance,


For if can help to find a solution:

Settings of the simulation
Rhombic dodecahedral box with SPC  water model was used. T= 300K, P=1bar
using a Berendsen thermostat (with time constant τt  = 0.1ps)-barostat with
an isotropic compressibility of 4.5·10-5 bar-1  and time constant of 0.5 ps.
Time step of 2 fs, constraining bond lengths with LINCS. For compute the
long range coulomb electrostatic, I use PME with a grid of 1Å. For the Van
der Waals interactions I use switch function between 0.8 and 0.9 nm.

How I do it
I minimize the energy of the solvated protein with the steepest descent
algorithm. Then I run a MD simulation at 300K using harmonic position
restraints on the heavy atoms of the protein with a force constant of 1000
KJ mol-1 nm-2. Then, I performe a simulating annealing from 0 to 300K and
fiinally, I run the "production" molecular dynamics starting from the SA

For analize the trajectory succesfully, I use the pbc nojump and fit
rot+trans options.

Melchor S. 

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