[gmx-users] Re: How to make carbon nanotube infinite?
Cun Zhang
apzc2529 at gmail.com
Wed Nov 25 02:32:26 CET 2009
Thank you, Justin !
I have add the output generated by grompp and mdrun at the end.
> Cun Zhang wrote:
> > hi, Justin. Thank you for your patience !
> >
> > I'm still in trouble with infinite CNT simulation.
> >
> > I'm trying to simulate the interaction of a infinite (16,0) CNT(CNT_A)
> > with 832 atoms and water. I'm using x2top to generate the CNT.itp with
> > share-bonds. The idea is that I generate a (16,0) CNT(CNT_B) with 960
> > atoms ( more 4 layer than CNT_A. Each layer has 32 atoms ).
> > When I use CNT.itp generated by CNT_A and x2top, it works. But when I
> > use the CNT.itp which has share-bonds information, it can't work.
> >
> >
> > The process I'm doing CNT simulation is as follows:
> > # the CNT_new.pdb is a (16,0) CNT with 960 atoms.
> > # I add the custom forcefield parameters to tmp.top, and change the
> > number of a charge group to 32, then rename it CNT.itp at the end.
> >
> > x2top -f CNT_new.pdb -o tmp.top -ff gmx -nopbc -nopairs -noparam -name
> > CNT
> >
> > bash sharebond_script # create share bonds
> >
>
> The script below is renumbering and removing atoms. Why are you doing
> this? I
> thought the purpose of CNT_new was to generate a larger structure?
>
I hope generate sharing bonds between the atoms at the top edge and the
atoms at the bottom edge of CNT by x2top. But the parameter -pbc does not
work. So I add 4 layers at the top of CNT.pdb and rename it CNT_new.pdb,
that is, the front 832 rows of them are same.
The atoms of No. 833-960 in CNT_new.pdb can be seen the bottom 4 layers of
atoms of No.1-128 of CNT.pdb translated up a box hight. So after generating
the topology file and renaming atoms of No. 833-960 to No.1-128 in the
topology file (use the command 'x2top -nopbc') the topology file of
CNT_new.pdb should be the same as the topology file of CNT.pdb with sharing
bonds (and angles, diherals) ( use the command 'x2top -pbc' ).
That's why I write that script. Hope you understand what I mean. Of course,
The other reason is that I'm not familar with how to generate CNT's topology
file, so I use x2top to do it. That's easier relatively.
> > editconf -f CNT.pdb -o -box 3.8 3.8 5.614
> >
>
> Now you are manipulating CNT.pdb - is this the correct next step? If this
> actually pertains to CNT_new.pdb, then the box size is insufficient to hold
> the
> larger structure. But now I'm just confused as to what you're doing.
>
This is the information when I run this command. I think it's ok.
system size : 1.270 1.270 5.472 (nm)
center : -0.000 0.000 2.736 (nm)
box vectors : 0.000 0.000 0.000 (nm)
box angles : 0.00 0.00 0.00 (degrees)
box volume : 0.00 (nm^3)
shift : 1.900 1.900 0.071 (nm)
new center : 1.900 1.900 2.807 (nm)
new box vectors : 3.800 3.800 5.614 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume : 81.07 (nm^3)
> > genbox -cp out -cs -p CNT -o b4em.pdb #The simulation box size can be
>
> > seen in b4em.pdb
> >
> > pymol b4em.pdb #remove water. After editing it,I save it as b4em.pdb
> > too.Now the information about box size is losing. I don't know why.I'm
> > not familar with it :)
> >
> > editconf -f b4em.pdb -o b4em -box 3.8 3.8 5.614 # Add the information
> > about box size
> > vim CNT.top #change the number of water to make it the same as
> b4em.pdb
> > grompp -f em -o em -c b4em -p CNT -maxwarn 5
> > mpirun -np 4 mdrun_mpi -v -s em -e em -o em -c after_em
>
> Does energy minimization work? What did the potential energy and maximum
> force
> converge to? Again, what is the purpose of "-maxwarn 5"? Are there errors
> that
> grompp is generating that you are simply trying to bypass? This is
> generally a
> bad idea.
>
Yes, EM work.
Steepest Descents converged to Fmax < 1000 in 9 steps
Potential Energy = -9.5444641e+04
Maximum force = 8.6610358e+02 on atom 832
Norm of force = 2.2713820e+02
There are two notes,no warnings,no errors when grompp.
When I run the MD,errors come:
500000 steps, 250.0 ps.
There were 64 inconsistent shifts. Check your topology
step 0
t = 0.003 ps: Water molecule starting at atom 7226 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
t = 0.004 ps: Water molecule starting at atom 7217 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
-------------------------------------------------------
Program mdrun, VERSION 4.0.5
Source code file: ../../../../src/mdlib/nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 200 ]
The output of grompp and mdrun are there.
cunzhang at Debian:~/CNT$ grompp -f em -o em -c b4em -p CNT -maxwarn 5
==help information==
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Opening library file /usr/share/gromacs/top/ffgmx.itp
Opening library file /usr/share/gromacs/top/ffgmxnb.itp
Opening library file /usr/share/gromacs/top/ffgmxbon.itp
Opening library file /usr/share/gromacs/top/ff_dum.itp
Generated 1337 of the 1540 non-bonded parameter combinations
Opening library file /usr/share/gromacs/top/spce.itp
Excluding 3 bonded neighbours molecule type 'CNT'
Excluding 2 bonded neighbours molecule type 'SOL'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
NOTE 1 [file CNT.top, line unknown]:
The largest charge group contains 32 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/share/gromacs/top/aminoacids.dat
There are: 2138 OTHER residues
There are: 0 PROTEIN residues
There are: 0 DNA residues
Analysing Other...
Making dummy/rest group for T-Coupling containing 7243 elements
Making dummy/rest group for Acceleration containing 7243 elements
Making dummy/rest group for Freeze containing 7243 elements
Making dummy/rest group for Energy Mon. containing 7243 elements
Making dummy/rest group for VCM containing 7243 elements
Number of degrees of freedom in T-Coupling group rest is 15315.00
Making dummy/rest group for User1 containing 7243 elements
Making dummy/rest group for User2 containing 7243 elements
Making dummy/rest group for XTC containing 7243 elements
Making dummy/rest group for Or. Res. Fit containing 7243 elements
Making dummy/rest group for QMMM containing 7243 elements
T-Coupling has 1 element(s): rest
Energy Mon. has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
NOTE 2 [file em.mdp, line unknown]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 2 Mb of data
writing run input file...
There were 2 notes
Back Off! I just backed up em.tpr to ./#em.tpr.2#
gcq#159: "Way to Go Dude" (Beavis and Butthead)
cunzhang at Debian:~/CNT$ mdrun -v -s em -e em -o em -c after_em
==help information==
Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file em.tpr, VERSION 4.0.5 (single precision)
Loaded with Money
Back Off! I just backed up em.trr to ./#em.trr.2#
Back Off! I just backed up em.edr to ./#em.edr.2#
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 1000
Step= 0, Dmax= 1.0e-02 nm, Epot= -9.12531e+04 Fmax= 1.74309e+03, atom=
824
Step= 1, Dmax= 1.0e-02 nm, Epot= -9.30129e+04 Fmax= 8.17086e+03, atom=
802
Step= 3, Dmax= 6.0e-03 nm, Epot= -9.43526e+04 Fmax= 2.00407e+03, atom=
827
Step= 5, Dmax= 3.6e-03 nm, Epot= -9.44415e+04 Fmax= 4.03472e+03, atom= 1
Step= 6, Dmax= 4.3e-03 nm, Epot= -9.47253e+04 Fmax= 3.99264e+03, atom=
802
Step= 8, Dmax= 2.6e-03 nm, Epot= -9.54446e+04 Fmax= 8.66104e+02, atom=
832
writing lowest energy coordinates.
Back Off! I just backed up after_em.gro to ./#after_em.gro.2#
Steepest Descents converged to Fmax < 1000 in 9 steps
Potential Energy = -9.5444641e+04
Maximum force = 8.6610358e+02 on atom 832
Norm of force = 2.2713820e+02
gcq#247: "Let's Unzip And Let's Unfold" (Red Hot Chili Peppers)
cunzhang at Debian:~/CNT$ grompp -f grompp -o pr -c after_em -p CNT -maxwarn 5
==help information==
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Ignoring obsolete mdp entry 'dihre-tau'
Ignoring obsolete mdp entry 'nstdihreout'
Ignoring obsolete mdp entry 'nstcheckpoint'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
processing topology...
Opening library file /usr/share/gromacs/top/ffgmx.itp
Opening library file /usr/share/gromacs/top/ffgmxnb.itp
Opening library file /usr/share/gromacs/top/ffgmxbon.itp
Opening library file /usr/share/gromacs/top/ff_dum.itp
Generated 1337 of the 1540 non-bonded parameter combinations
Opening library file /usr/share/gromacs/top/spce.itp
Excluding 3 bonded neighbours molecule type 'CNT'
Excluding 2 bonded neighbours molecule type 'SOL'
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
NOTE 1 [file CNT.top, line unknown]:
The largest charge group contains 32 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/share/gromacs/top/aminoacids.dat
There are: 2138 OTHER residues
There are: 0 PROTEIN residues
There are: 0 DNA residues
Analysing Other...
Making dummy/rest group for Acceleration containing 7243 elements
Making dummy/rest group for Freeze containing 7243 elements
Making dummy/rest group for Energy Mon. containing 7243 elements
Making dummy/rest group for VCM containing 7243 elements
Number of degrees of freedom in T-Coupling group System is 15315.00
Making dummy/rest group for User1 containing 7243 elements
Making dummy/rest group for User2 containing 7243 elements
Making dummy/rest group for XTC containing 7243 elements
Making dummy/rest group for Or. Res. Fit containing 7243 elements
Making dummy/rest group for QMMM containing 7243 elements
T-Coupling has 1 element(s): System
Energy Mon. has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
NOTE 2 [file grompp.mdp, line unknown]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 143 Mb of data
writing run input file...
There were 2 notes
Back Off! I just backed up pr.tpr to ./#pr.tpr.1#
gcq#97: "The Universe is Somewhere In Here" (J.G.E.M. Fraaije)
cunzhang at Debian:~/CNT$ mdrun -v -s pr -e pr -o pr -c after_pr
==help information==
Back Off! I just backed up md.log to ./#md.log.3#
Getting Loaded...
Reading file pr.tpr, VERSION 4.0.5 (single precision)
Loaded with Money
There were 64 inconsistent shifts. Check your topology
Back Off! I just backed up pr.trr to ./#pr.trr.1#
Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
Back Off! I just backed up pr.edr to ./#pr.edr.1#
starting mdrun 'Pure Water in water'
500000 steps, 250.0 ps.
There were 64 inconsistent shifts. Check your topology
step 0
t = 0.003 ps: Water molecule starting at atom 7226 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
t = 0.004 ps: Water molecule starting at atom 7217 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
-------------------------------------------------------
Program mdrun, VERSION 4.0.5
Source code file: ../../../../src/mdlib/nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 200 ]
-------------------------------------------------------
"Right Now My Job is Eating These Doughnuts" (Bodycount)
Cun Zhang
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