[gmx-users] errors on carbon nanotube
jackyxh at 163.com
jackyxh at 163.com
Sat Jun 24 05:52:44 CEST 2006
Hi,GMX group and other users:
I am a gromacs(version 3.3) user. I want to do carbon nanotube(CNT) MD.
Months ago, when I ran grompp, she told me that something was wrong.
(see http://www.gromacs.org/pipermail/gmx-users/2006-April/021092.html)
After i got suggestions from GMX group and other users (really thank Bob
who has given me some importent advices!) and checked almost
all of the "Mailing lists" about CNT, i began other ways to generate
my files (.gro .top and so on).
This morning i got the results of my working----ERRORS!
So I type this for help AGAIN.
I will tell what I have done in details, may anyone could give me a hand.
<What i have?>
a "cnt.pdb" and a "cnt.gro" which i write by myself on the base of "cnt.pdb"
<What i need?>
A stable structure ----"cnt.top"
<What i have tried?>
(A) PRODRG (B) WRITE "cnt.top" MANUALLY <C> x2top
(A) PRODRG
when i input my cnt.pdb, it told me something like "the atoms C are not in same plane".
so i gave it up.
(B) WRITE "cnt.top" MANUALLY
After checked most of the "Mailing lists" about CNT, i began my work as follows:
a. write cntbon.itp for c-c bond forcefield of the CNT
b. write cntnb.itp for nonbond forcefield of the CNT
c. write cnt.itp for the CNT molecule structure
d. include files in a. b. c. into "cnt.top"
Am i on the right way? if so, i will show how the files look like,
=========================================================================
*****a. the cntbon.itp
------------------------------------------------
[ bondtypes ]
; i j func b0 D bata
C C 3 0.14200 478900 21.867
[ angletypes ]
; i j k func th0 cth
C C C 1 120.000 418.400
[ dihedraltypes ]
; j k func phi0 cp mult
C C 1 180.000 12.060 2
------------------------------------------------
*****b. the cntnb.itp
------------------------------------------------
[ atomtypes ]
;name mass charge ptype c6 c12
C 12.01100 0.000 A 0.57353E-02 0.18707E-05
[ nonbond_params ]
; i j func c6 c12
C C 1 0.57353E-02 0.18707E-05
[ pairtypes ]
; i j func cs6 cs12
C C 1 0.57353E-02 0.18707E-05
------------------------------------------------
*****c. cnt.itp
===========================
[ moleculetype ]
; molname nrexcl
CNT 4
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 C 1 CNT C1 0 0 12
2 C 1 CNT C2 1 0 12
...
59 C 1 CNT C59 58 0 12
60 C 1 CNT C60 59 0 12
[ bonds ]
; ai aj funct b0 D bata
1 2 3 0.142 478900 21.867
1 20 3 0.142 478900 21.867
2 11 3 0.142 478900 21.867
.
.
[ pairs ]
; ai aj funct c6 12
1 10 1 0 0
2 3 1 0 0
4 5 1 0 0
.
.
[ angles ]
; ai aj ak funct th0 cth
1 2 11 1 118.35 418.4
3 4 13 1 118.35 418.4
1 20 29 1 120 418.4
3 12 21 1 120 418.4
.
.
[ dihedrals ]
; ai aj ak al funct
1 20 19 10 1
2 11 12 3 1
4 13 14 5 1
6 15 16 7 1
.
.
.
===========================
*****d. cnt.top
--------------------------------------------------
#include "ffgmx.itp"
#include "cntbon.itp"
#include "cntnb.itp"
#include "cnt.itp"
[ system ]
;Name
cnt-with-5-by-5
[ molecules ]
;Molecule name Number of molecules
CNT 1
----------------------------------------------------
******e. The cnt.gro
===================================
"These are the 005005060 single walled carbon nanotube's xyz by jacky" (jacky allon)
60
1CNT C1 1 0.3390 0.0000 0.0000 1 0
..
1CNT C10 10 0.2268 -0.2519 0.0000 1 0
1CNT C11 11 0.2743 0.1993 0.1230 1 0
..
1CNT C20 20 0.3316 -0.0705 0.1230 1 0
1CNT C21 21 0.1048 0.3224 0.2460 1 0
..
1CNT C30 30 0.3097 0.1379 0.2460 1 0
1CNT C31 31 -0.1048 0.3224 0.3689 1 0
..
1CNT C40 40 0.1695 0.2936 0.3689 1 0
1CNT C41 41 -0.2743 0.1993 0.4919 1 0
..
1CNT C50 50 -0.0354 0.3371 0.4919 1 0
1CNT C51 51 -0.3390 0.0000 0.6149 1 0
..
1CNT C60 60 -0.2268 0.2519 0.6149 1 0
2.4596 2.4596 2.4596
===================================
******f. The em.mdp
===================================
;
; Input file
;
cpp = /usr/bin/cpp
define = -DFLEX_SPC
integrator = steep
constraints = none
integrator = steep
nsteps = 1000
;
; Energy minimizing stuff
;
emtol = 2000
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
=============================================================================
e. Run the grompp for EM
[root at localhost cnt0621]# grompp -f em.mdp -c cnt.gro -p cnt.top -o
.
.
creating statusfile for 1 node...
' for variable integrator, using 'md'
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'
' for variable ns-type, using 'Grid'
Next time use one of: 'Grid' 'Simple'
' for variable tcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen' 'Andersen-
interval'
' for variable Pcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'
' for variable gen-vel, using 'no'
Next time use one of: 'no' 'yes'
' for variable constraints, using 'none'
Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
WARNING 1 [file em.mdp, line unknown]:
Unknown left-hand 'integrator' in parameter file
checking input for internal consistency...
...ling /usr/bin/cpp
: 没有那个文件或目录/cpp (No that file or directory /cpp)
cpp exit code: 32512
5x-60.top > gromppUhFDce' -DFLEX_SPC
' command is defined in the .mdp file
processing topology...
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: grompp.c, line: 427
Fatal error:
number of coordinates in coordinate file (5x-60.gro, 60)
does not match topology (5x-60.top, 0)
-------------------------------------------------------
"Fly to the Court of England and Unfold" (Macbeth, Act 3, Scene 6, William Shake
speare)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>There are two points i cannot understand:
>1st, when i did not mention"integrator=steep", grompp told me "using 'md'".
> why she still showed me the same message when i add "ntegrator=steep"?
>(someone said this may be because grompp did not recognize some format of .mdp file. What's that?)
>2nd,Fatal error:
> number of coordinates in coordinate file (5x-60.gro, 60)
> does not match topology (5x-60.top, 0)
> How could i make some changes to fix this ERROR? i am completely confused here.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
<C> x2top
i also tried x2top to generate the .top file. But when i tried x2top:
[root at localhost cnt0621]# x2top -f cnt.gro -o cnt.top -pbc
.
.
choose 7: [DEPRECATED] Gromacs force field (see manual)
.
Looking whether force field file ffgmx.rtp exists
Opening library file /usr/share/gromacs/top/ffgmx.rtp
Generating bonds from distances...
Opening library file /usr/share/gromacs/top/ffgmx.atp
There are 53 type to mass translations
atom 60
Opening library file /usr/share/gromacs/top/ffgmx.n2t
There are 23 name to type translations
-------------------------------------------------------
Program x2top, VERSION 3.3
Source code file: x2top.c, line: 239
Fatal error:
No forcefield type for atom 1 (1) with 1 bonds
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>upto this error, i changed the unit of the cnt.gro from nm to Angstrom (should? should not?)
>so that the file looks like
>------------------------------------------------------
> "These are the 005005060 single walled carbon nanotube's xyz by jacky" (jacky allon)
>60
>1CNT C1 1 3.390 0.0000 0.0000 1 0
>..
>1CNT C10 10 2.268 -2.519 0.0000 1 0
>1CNT C11 11 2.743 1.993 1.230 1 0
>.
>.
>------------------------------------------------------
>
>then x2top gave another error as:
>....
>....
>Looking whether force field file ffgmx.rtp exists
>Opening library file /usr/share/gromacs/top/ffgmx.rtp
>-------------------------------------------------------
>Program x2top, VERSION 3.3
>Source code file: confio.c, line: 709
>
>Fatal error:
>Invalid line in cnt.gro for atom 1:
>1CNT C2 2 3.097 1.379 0.000
>-------------------------------------------------------
>
>So, what's that? A format error again or something else? How should i do to fix that?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
That's all, i have tried 3 ways, and got more errors!
Can any one help me over these?!
Thanking you!
Jacky Allon
jackyxh at 163.com
--
If you send me one, I will always Re you three, friendship, help or anything else except emails and money:) ――Jacky Allon
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