[gmx-users] Gromacs - Dimer Simulation problems
Michael Carter
Michael.Carter at icr.ac.uk
Tue Jul 15 13:30:55 CEST 2014
Hi Kavya,
That worked perfectly. Thank you.
Cheers,
Michael
On 15/07/2014 11:43, "Kavyashree M" <hmkvsri at gmail.com> wrote:
>Hi Michael,
>
>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.
>
>Good luck
>kavya
>
>
>
>On Tue, Jul 15, 2014 at 3:58 PM, Michael Carter <Michael.Carter at icr.ac.uk>
>wrote:
>
>>
>> Hi,
>>
>> 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
>> #endif
>>
>> ; 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)
>> constrained
>> 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
>> electrostatics
>> 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
>> accurate
>> 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
>> NPT
>> pcoupltype = isotropic ; uniform scaling of box
>> vectors
>> 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
>> disk.
>>
>> 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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