[gmx-users] Gromacs - Dimer Simulation problems
hmkvsri at gmail.com
Tue Jul 15 12:43:07 CEST 2014
This used to happen in my simulations also. Try using nojump for your
xtc file and re-plot the rmsd. I presume the jump that you see in your
rmsd is a sudden jump and not a gradual one. If its a sudden jump then
this will solve the problem. if you observe your simulation in ngmx you
can see that at the point where rmsd jumps, one of your monomer might
go outside the box.
Try this and see.
On Tue, Jul 15, 2014 at 3:58 PM, Michael Carter <Michael.Carter at icr.ac.uk>
> I have been running a short MD simulation (100ns) on a dimer protein. The
> two monomers are identical, after looking into your suggestions on
> http://www.gromacs.org/Documentation/How-tos/Multiple_Chains I have set
> up the system with waters and ions. The topol.top to look like this:
> ; File 'topol.top' was generated
> ; By user: michaelc (1128283773)
> ; On host: 104844CTHDT.local
> ; At date: Tue Jul 1 12:30:36 2014
> ; This is a standalone topology file
> ; It was generated using program:
> ; pdb2gmx - VERSION 4.6.5
> ; Command line was:
> ; /usr/local/gromacs/bin/pdb2gmx -f BCL6_584_pseudo_apo.pdb -o
> BCL6_584_pseudo_apo.gro -water tip3p -ignh
> ; Force field was read from the standard Gromacs share directory.
> ; Include forcefield parameters
> #include "amber99sb.ff/forcefield.itp"
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Protein_chain_B.itp"
> ; Include water topology
> #include "amber99sb.ff/tip3p.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> ; Include topology for ions
> #include "amber99sb.ff/ions.itp"
> [ system ]
> ; Name
> BCL6_584_pseudo_apo in water
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> Protein_chain_B 1
> SOL 40832
> NA 76
> CL 79
> I have then run a short minimisation and equilibration which ran
> successfully. I then ran a production MD run of 100ns. The md.mdp looks
> like this:
> title = Protein-ligand complex MD simulation
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 50000000 ; 2 * 50000000 = 100000 ps (100 ns)
> dt = 0.002 ; 2 fs
> ; Output control
> nstxout = 0 ; suppress .trr output
> nstvout = 0 ; suppress .trr output
> nstenergy = 1000 ; save energies every 2 ps
> nstlog = 1000 ; update log file every 2 ps
> nstxtcout = 1000 ; write .xtc trajectory every 2 ps
> energygrps = System
> ; Bond parameters
> continuation = yes ; first dynamics run
> constraint_algorithm = lincs ; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> rlist = 0.9 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> ; Temperature coupling
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = Protein Water_and_ions ; two coupling groups - more
> tau_t = 0.1 0.1 ; time constant, in ps
> ref_t = 300 300 ; reference temperature, one
> for each group, in K
> ; Pressure coupling
> pcoupl = Parrinello-Rahman ; pressure coupling is on for
> pcoupltype = isotropic ; uniform scaling of box
> tau_p = 2.0 ; time constant, in ps
> ref_p = 1.0 ; reference pressure, in bar
> compressibility = 4.5e-5 ; isothermal compressibility
> of water, bar^-1
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = no ; assign velocities from Maxwell distribution
> After this simulation finished I obtained the resultant .xtc and .tpr
> files. The system was then corrected to remove any problems of drifting
> cause by PBC and the system was centered on the protein. This was done
> using the following commands:
> trjconv -s md_0_100.tpr -f md_0_100.xtc -o protein.xtc
> tpbconv -s md0_100.tpr -o protein.tpr
> Choosing the group 1 (Protein).
> trjconv -s protein.tpr -f protein.xtc -o protein.gro -dump 0
> Choosing the group 1 (Protein).
> trjconv -s protein.tpr -f protein.xtc -o protein_fit.xtc -fit rot+trans
> Chossing the group 4 (Backbone) and the system 1 (Protein) to write to
> After analysing the output it appears that after around 50ns something
> very strange happens and my simulation see a large jump in RMSD to over 5A.
> This continues to happen for the last 40ns of the simulation. Upon
> visualisation it would appear that the dimer dissociates into two monomers.
> There is no real reason for this and it appears to happen randomly for the
> last 50 ns of the simulation.
> Have you come across this problem before? Do you think that I should apply
> some constraints to stop this from happening? Or could it be that I need to
> adjust my system setup to remove this issue?
> Any help on this matter would be greatly appreciated.
> All the best,
> Michael Carter
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> Company Limited by Guarantee, Registered in England under Company No.
> 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
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