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. 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.
Are they overlapping only after minimization, or does the starting configuration
contain clashes? Atoms should not be significantly displaced during EM, so I'd
be inclined to believe the starting structure is the problem.
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.
Simplify the system. Rather than dealing with a full box of ethane, try
minimizing one molecule, then a few (like 2 or 4) in a box, then build up. If
these small systems are stable, then the topology and .mdp are fine (though some
of your cutoffs look strange to me). Then build your target system once you've
verified that all the pieces should be working together.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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