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) [EMAIL PROTECTED]
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