[gmx-users] A question about simulating a box of ethane in GROMACS
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Sep 6 16:59:26 CEST 2011
On 7/09/2011 12:40 AM, Phil (Yang) Song wrote:
> Hi, all
>
> I am learning GROMACS 4.5.1 recently and encountered a problem that
> puzzled me for weeks. I am wondering if someone can help me with this.
>
> Here is the problem: I was trying to perform a MD simulation for 216
> ethane molecules in a box. I have first generated a box of ethane with
> random position and orientation.
That's almost certainly inappropriate. Atomic clashes are inevitable,
and EM will not fix severe problems.
Get a single molecule in a small box, and use genconf to replicate it.
Then use EM and equilibrate thoroughly to remove the residual ordering.
Judicious use of NPT will fix your density to whatever you want.
Mark
> Then, I wanted to run a minimization for the box of ethane to get rid
> of close contact of the randomly ethane molecules. However, I have
> found that some of the ethane molecules laid on top of each other
> after minimization and infinity forces were resulted.
>
> Since my mdp file was successfully used to generate other type of
> molecules such as acetylene and ethylene and they should be correct.
> Also, I have tried to use conjugate gradient instead of steepest
> decent for the minimization, but this effort came out to be in vain.
>
> Later, I thought the topology file should be the source of error. I
> have carefully checked the topology file for couple of times but did
> not find any obvious error. I have also tried to change the charges on
> each atom in the ethane to 0 and then run the minimization. Again, the
> ethane was attracted into each other. Hence, I think the vdw could be
> the problem. However, the parameters of the vdw interaction are all
> from the opls-aa files that come with gromacs and it should be fine.
>
> Eventually, I am puzzled...
>
> I am iterating the content of the content of mdp input file and itp
> file in the email and also attaching the input and output of my result
> as a tarball. Hope someone can help me to solve this problem.
>
> Thank you in advance!
>
> Best,
> Phil Song
>
> ================================================================================
> MDP file
>
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> ; preprocessing options
>
> ; title of the simulation
> title =
>
> ; include path
> include =
>
> ; cpp flag
> define =
>
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> ; energy minimization
> integrator = steep
>
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.001
> nsteps = 500
>
> ; run continuation or reperforming
> init_step = 0
>
> emtol = 1000.0
> emstep = 0.01
>
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> ; periodic boundary conditions
> pbc = xyz
>
> periodic_molecules = no
>
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> ; electrostatics and vdw options
> ; electrostatics method
> coulombtype = PME
> rcoulomb = 1.3
>
> ; fourier setup for PME
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
>
> ewald_geometry = 3d
>
> ; vdw cutoff
> rvdw-switch = 0
> rvdw = 1.31
>
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> ; neighbor list options
> ; neighbor list frequency
> nstlist = 10
>
> ; neighbor search algorithm
> ns_type = grid
>
> ; neighbor list cut-off
> rlist = 1.30
>
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> ; thermostat and barostat
> tcoupl = v-rescale
> tc_grps = System
> ref_t = 50.5
> tau_t = 0.5
>
> pcoupl = berendsen
> pcoupltype = isotropic
> nstpcouple = 10
> ref_p = 1.01325
> tau_p = 1.0
>
> ; Using compressibility of ethanol at 273.1 (approximately)
> ; from J. Phys. Chem., 1963, 67 (10), pp 2160.2164
>
> compressibility = 1.0e-5
>
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> ; velocty generation
> gen_vel = yes
> gen_temp = 50.5
> ; gen_seed = 173529
>
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> ; output control options
> ; output frequency for coords, velocities and forces
> nstxout = 5000
> nstvout = 5000
> nstfout = 5000
>
> ; output frequency for energy
> nstenergy = 5000
> ; energygrps =
>
> ; output frequency for log
> nstlog = 5000
>
> ; output options for trajectory
> nstxtcout = 5000
> xtc_precision = 100000
> ; xtc_grps =
>
>
> ================================================================================
> ITP file
>
> ; Ethane:
> ; Assign of the atom index
> ;
> ; H2 H6
> ; | |
> ; H3 - C1 - C5 - H7
> ; | |
> ; H4 H8
> ;
>
> [ moleculetype ]
> ; name nrexcl
> Ethane 3
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge
> mass
> 1 opls_135 1 ETH CE1 1 -0.18
> 2 opls_140 1 ETH HE2 1 0.06
> 3 opls_140 1 ETH HE3 1 0.06
> 4 opls_140 1 ETH HE4 1 0.06
> 5 opls_135 1 ETH CE5 2 -0.18
> 6 opls_140 1 ETH HE6 2 0.06
> 7 opls_140 1 ETH HE7 2 0.06
> 8 opls_140 1 ETH HE8 2 0.06
>
> [ bonds ]
> ; ai aj funct c0 c1
> 1 5 1
> 2 1 1
> 3 1 1
> 4 1 1
> 6 5 1
> 7 5 1
> 8 5 1
>
> [ pairs ]
> ; ai aj funct
> 2 6
> 2 7
> 2 8
> 3 6
> 3 7
> 3 8
> 4 6
> 4 7
> 4 8
>
> [ angles ]
> ; ai aj ak funct c0 c1
> ; H3-C-C
> 2 1 5 1
> 3 1 5 1
> 4 1 5 1
> ; H-C-H
> 2 1 3 1
> 2 1 4 1
> 3 1 4 1
> ; C-C-H3
> 6 5 1 1
> 7 5 1 1
> 8 5 1 1
> ; H-C-H
> 6 5 7 1
> 6 5 8 1
> 7 5 8 1
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2
> c3 c4
> 2 1 5 6 3
> 3 1 5 6 3
> 4 1 5 6 3
> 2 1 5 7 3
> 3 1 5 7 3
> 4 1 5 7 3
> 2 1 5 8 3
> 3 1 5 8 3
> 4 1 5 8 3
>
>
>
> --
> Phil (Yang) Song
> Room 509, 590 Comm. Ave.
> Chem. Dept., Boston Univ.
> Boston, MA, 02215, USA
>
>
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