[gmx-users] Problem calculating RMSD with gromos

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jul 2 14:53:09 CEST 2013

Hi Melchor,

So what did you expect, what did you do, and what did you get?



On Tue, Jul 2, 2013 at 2:45 PM, Melchor S. <msmqbm at cid.csic.es> wrote:

> 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
> ff?
> Thanks in advance,
> PD:
> 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
> trajectory.
> For analize the trajectory succesfully, I use the pbc nojump and fit
> rot+trans options.
> Melchor S.
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Tsjerk A. Wassenaar, Ph.D.

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