[gmx-users] Constraints applied for keeping rigid in ND
hang yin
yinhang503 at gmail.com
Mon Apr 20 18:34:54 CEST 2015
Hi Alex,
Thanks for your reply.
I used large time step because it is the default value(20 ~40 ps) for the
Martini Coarse Grained ff. Applied that large time step, the angles and
bonds have been proved that they could not keep ND rigid enough. And for a
very large system I want to build in future, the CG model have to be used,
meaning that I have to solve the rigidity problem in a large time step
setup. Hence I really want to use constraints here.
Hang
2015-04-21 0:22 GMT+08:00 Alex <nedomacho at gmail.com>:
> Also, I just looked at your topology. Where are your angles? Try to
> implement them and then turn off constraints.
>
> Alex
>
>
> A> Is there a particular reason you're applying LINCS constraints to your
> A> diamond structure? Usually, LINCS gives convergence
> A> errors/warnings if the system is poorly
> A> equilibrated and/or your time step is too large. The fact that your
> A> system was "soft" without constraints actually suggests poor setup,
> A> which once again could include the time step.
>
> A> Diamond structure, if properly set up, should be quite rigid, even if
> A> your bond/angle terms are somewhat off, because, well, it's the
> A> diamond structure.
>
> A> Alex
>
>
> hy>> Hi all,
>
> hy>> My research focuses on the dynamics of a nanodiamond(ND) in a
> biological
> hy>> environment. I am working with gromacs version 5.0.2 and using
> Martini CG
> hy>> ff. In order to keep the rigidity of ND, I applied constraints as the
> stiff
> hy>> bond in the .itp file. But my system crashed in the NVT run with LINCS
> hy>> WARNING. So I tried to use a small ND, an octahedron, in the water
> box for
> hy>> debugging. It did work well. However, after I increased its size(just
> add 3
> hy>> beads actually), it crashed with same input parameters.
>
> hy>> How it could happen? I am the beginner using gromacs and CG model. I
> think
> hy>> the problem is due to the constraints because the same system with
> defined
> hy>> bond interaction worked well(but the ND in this situation is soft). I
> am
> hy>> just wondering that is there any limitation for applying constraints
> for
> hy>> crystal packing system or anything wrong with my configuration?
>
> hy>> Seeking for help. Thanks a lot.
>
> hy>> Kevin
> hy>>
> ******************************************************************************
> hy>> My itp file:
>
> hy>> ;itp file of ND
> hy>> [ moleculetype ]
> hy>> ; molname nrexcl
> hy>> CG-ND 1
>
> hy>> [ atoms ]
> hy>> ; id type resnr residu atom cgnr charge
> hy>> 1 P1 1 FO CD1 1 0.000000
> hy>> 2 C1 1 FH CD2 2 0.000000
> hy>> 3 P1 1 FO CD3 3 0.000000
> hy>> 4 C1 1 FH CD4 4 0.000000
> hy>> 5 C1 2 FH CD1 5 0.000000
> hy>> 6 C1 2 FH CD2 6 0.000000
> hy>> 7 C1 2 FH CD3 7 0.000000
> hy>> 8 P1 2 FO CD4 8 0.000000
> hy>> 9 P1 3 FO CD1 9 0.000000
> hy>> 10 P1 3 FO CD2 10 0.000000
>
> hy>> [ constraints ]
> hy>> ; i j funct length force.c.
>
> hy>> #ifdef FLEXIBLE
> hy>> [ bonds ]
> hy>> #endif
>
> hy>> 1 2 1 0.317 1000000
> hy>> 1 3 1 0.317 1000000
> hy>> 1 4 1 0.317 1000000
> hy>> 2 3 1 0.317 1000000
> hy>> 2 4 1 0.317 1000000
> hy>> 3 4 1 0.317 1000000
> hy>> 3 5 1 0.317 1000000
> hy>> 3 6 1 0.317 1000000
> hy>> 4 5 1 0.317 1000000
> hy>> 4 6 1 0.317 1000000
> hy>> 5 6 1 0.317 1000000
> hy>> 5 7 1 0.317 1000000
> hy>> 5 8 1 0.317 1000000
> hy>> 6 7 1 0.317 1000000
> hy>> 6 8 1 0.317 1000000
> hy>> 7 10 1 0.317 1000000
> hy>> 7 8 1 0.317 1000000
> hy>> 7 9 1 0.317 1000000
> hy>> 8 10 1 0.317 1000000
> hy>> 8 9 1 0.317 1000000
> hy>> 9 10 1 0.317 1000000
> hy>>
> ******************************************************************************
> hy>> My mdp file:
>
> hy>> title = debugging for ND
> hy>> ; Run parameters
> hy>> integrator = md ; leap-frog integrator
> hy>> nsteps = 2500 ; 20 * 2500 = 500 ps (0.05 ns)
> hy>> dt = 0.02 ; 20 fs
> hy>> ; Output control
> hy>> nstxout = 1 ; save coordinates
> hy>> nstvout = 1 ; save velocities
> hy>> nstenergy = 10 ; save energies
> hy>> nstlog = 10 ; update log file
> hy>> nstcomm = 10
> hy>> fcstep = 0
> hy>> nstcalcenergy = 10
>
> hy>> ; Bond parameters
> hy>> unconstrained_start = no
> hy>> constraints = none
> hy>> constraint_algorithm = Lincs
> hy>> lincs_order = 4
> hy>> lincs_warnangle = 30
> hy>> lincs-iter = 1
> hy>> morse = no
>
> hy>> ; Neighborsearching
> hy>> cutoff-scheme = verlet
> hy>> verlet-buffer-drift = 0.001
> hy>> ns_type = grid ; search neighboring grid cels
> hy>> nstlist = 10 ;
> hy>> rlist = 1.4 ; short-range neighborlist cutoff (in nm)
> hy>> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
> hy>> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
> hy>> vdw_type = cutoff
> hy>> rvdw_switch = 0.9
> hy>> vdw-modifier = Potential-shift
>
> hy>> ; Electrostatics
> hy>> coulombtype = Reaction_field
> hy>> coulomb_modifier= Potential-shift
> hy>> rcoulomb_switch = 0.0
> hy>> epsilon_r = 15
> hy>> epsilon_rf = 0
>
> hy>> ; Temperature coupling is on
> hy>> tcoupl = Berendsen
> hy>> tc-grps = system ; three coupling groups - more accurate
> hy>> tau_t = 1.0 ; time constant, in ps
> hy>> ref_t = 310 ; reference temperature, one for each group, in K
> hy>> ; Pressure coupling is on
> hy>> pcoupl = no ; Pressure coupling on in NPT
> hy>> pcoupltype = isotropic ; uniform scaling of x-y-z box vectors
> hy>> tau_p = 4.0 ; time constant
> hy>> ref_p = 1.0 ; reference pressure
> hy>> compressibility = 1e-5 ; isothermal compressibility, bar^-1
>
> hy>> ; Periodic boundary conditions
> hy>> pbc = xyz ; 3-D PBC
>
> hy>> ; Velocity generation
> hy>> gen_vel = no
> hy>> gen_temp = 310
> hy>> gen_seed = -1
>
>
>
>
>
>
>
> --
> Best regards,
> Alex mailto:nedomacho at gmail.com
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list