[gmx-users] n-hexadecane simulation
Frederic Leroy
frederic.leroy at urv.net
Mon Sep 18 17:00:17 CEST 2006
You could change the lincs_iter. I would use SHAKE rather than LINCS.
For n-alkanes using the model of Ryckaert-Bellemans, it is OK. Anyway,
2fs is correct.
Jae Hyun Park wrote:
>Dear all GROMACS users:
>
>I'm simulating n-hexadecane bulk at 300 K using UA model with fixed bond length, harmonic angle potential, and Rychaert-Bellemans torsion model. However, it is so unstable for 2fs time step - The bond length suddenly diverges. The simulation becomes stable for 0.2 fs time step, which seems too small. Could anybody give an instruction for this problem? Followings are my .mdp and topology files.
>
>Thank you in advance for your kind instruction.
>
>
>; VARIOUS PREPROCESSING OPTIONS =
>title = 2*2 pore
>cpp = /lib/cpp
>
>integrator = md
>dt = 0.002
>nsteps = 6000000
>nstcomm = 1
>
>nstxout = 1000
>nstvout = 1000
>nstfout = 1000
>nstlog = 1000
>nstenergy = 1000
>
>;Output frequency and precision for xtc file =
>nstxtcout = 500
>xtc_precision = 10000
>xtc-grps = HEX
>
>; CONSTRAINT SCHEME
>constraints = all-bonds
>constraint_algorithm = lincs
>
>; Selection of energy groups =
>energygrps = HEX
>
>; NEIGHBORSEARCHING PARAMETERS =
>nstlist = 10
>ns_type = grid
>pbc = xyz
>
>; OPTIONS FOR WEAK COUPLING ALGORITHMS =
>tcoupl = nose-hoover
>tc-grps = HEX
>tau_t = 0.3
>ref_t = 300.0
>
>rcoulomb = 1.49
>rlist = 1.38
>rvdw = 1.38
>
> ; GENERATE VELOCITIES FOR STARTUP RUN =
>gen_vel = yes
>gen_temp = 300.0
>gen_seed = 94729
>
>[ moleculetype ]
>; molname nrexcl
>HEX 3
>
>[ atoms ]
>; nr type resnr residue atom cgnr charge
> 1 CH3 1 HEX C1 1 0.000
> 2 CH2 1 HEX C2 1 0.000
> 3 CH2 1 HEX C3 1 0.000
> 4 CH2 1 HEX C4 1 0.000
> 5 CH2 1 HEX C5 1 0.000
> 6 CH2 1 HEX C6 1 0.000
> 7 CH2 1 HEX C7 1 0.000
> 8 CH2 1 HEX C8 1 0.000
> 9 CH2 1 HEX C9 1 0.000
> 10 CH2 1 HEX C10 1 0.000
> 11 CH2 1 HEX C11 1 0.000
> 12 CH2 1 HEX C12 1 0.000
> 13 CH2 1 HEX C13 1 0.000
> 14 CH2 1 HEX C14 1 0.000
> 15 CH2 1 HEX C15 1 0.000
> 16 CH3 1 HEX C16 1 0.000
>
>[ constraints ]
> 1 2 2 0.153
> 2 3 2 0.153
> 3 4 2 0.153
> 4 5 2 0.153
> 5 6 2 0.153
> 6 7 2 0.153
> 7 8 2 0.153
> 8 9 2 0.153
> 9 10 2 0.153
> 10 11 2 0.153
> 11 12 2 0.153
> 12 13 2 0.153
> 13 14 2 0.153
> 14 15 2 0.153
> 15 16 2 0.153
>
>[ angles ]
> 1 2 3 1 114.0 519.6875
> 2 3 4 1 114.0 519.6875
> 3 4 5 1 114.0 519.6875
> 4 5 6 1 114.0 519.6875
> 5 6 7 1 114.0 519.6875
> 6 7 8 1 114.0 519.6875
> 7 8 9 1 114.0 519.6875
> 8 9 10 1 114.0 519.6875
> 9 10 11 1 114.0 519.6875
> 10 11 12 1 114.0 519.6875
> 11 12 13 1 114.0 519.6875
> 12 13 14 1 114.0 519.6875
> 13 14 15 1 114.0 519.6875
> 14 15 16 1 114.0 519.6875
>
>[ dihedrals ]
> 1 2 3 4 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0
> 2 3 4 5 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0
> 3 4 5 6 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0
> 4 5 6 7 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0
> 5 6 7 8 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0
> 6 7 8 9 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0
> 7 8 9 10 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0
> 8 9 10 11 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0
> 9 10 11 12 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0
> 10 11 12 13 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0
> 11 12 13 14 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0
> 12 13 14 15 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0
> 13 14 15 16 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0
>=======================================
>Jae Hyun Park, Ph.D.
>Postdoctoral Associate
>3221 Beckamn Institute
>University of Illinois at Urbana-Champaign
>405 North Mathews Avenue
>Urbana, IL 61801
>(Tel) 217-244-4353, (FAX) 217-244-4333
>(E-mail) jaepark at uiuc.edu
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