[gmx-users] Re: Regarding Na ions
naga raju
nagaraju_cy at yahoo.co.in
Fri Jul 6 06:50:38 CEST 2007
Dear gmx users,
I am thankful to Dr.Mark and Dr.Osmair for
their responce to my queries. As per their suggestion,
I checked ions.itp file in that sodium atoms are
represented by NA+ in opls force field. I am using
gromacs 3.3.1 version.
[moleculetype ]
; molname nrexcl
NA+ 1
[ atoms ]
; id at type res nr residu name at name cg nr
charge mass
1 opls_407 1 NA+ NA 1 1 22.98977
As per Dr.Osmair suggestion, I built a sodium.itp
file, the file was shown below.
ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
[ moleculetype ]
; NAme nrexcl
NA+ 1
[ atoms ]
; nr type resnr residue atom cgnr
charge mass typeB chargeB massB
1 opls_407 1 NA+ NA 1
1 22.9898 ; qtot 1
2 opls_407 2 NA+ NA 2
1 22.9898 ; qtot 2
3 opls_407 3 NA+ NA 3
1 22.9898 ; qtot 3
4 opls_407 4 NA+ NA 4
1 22.9898 ; qtot 4
5 opls_407 5 NA+ NA 5
1 22.9898 ; qtot 5
6 opls_407 6 NA+ NA 6
1 22.9898 ; qtot 6
7 opls_407 7 NA+ NA 7
1 22.9898 ; qtot 7
8 opls_407 8 NA+ NA 8
1 22.9898 ; qtot 8
9 opls_407 9 NA+ NA 9
1 22.9898 ; qtot 9
10 opls_407 10 NA+ NA 10
1 22.9898 ; qtot 10
11 opls_407 11 NA+ NA 11
1 22.9898 ; qtot 11
12 opls_407 12 NA+ NA 12
1 22.9898 ; qtot 12
.........
..........
..........
and also tried with the fallowing type...
[ moleculetype ]
; Name nrexcl
Sodium 1
[ atoms ]
; nr type resnr residue atom cgnr
charge mass typeB chargeB massB
1 opls_405 1 Na Na 1
1 35.4530 ; qtot 1
2 opls_405 2 Na Na 2
1 35.4530 ; qtot 2
3 opls_405 3 Na Na 3
1 35.4530 ; qtot 3
4 opls_405 4 Na Na 4
1 35.4530 ; qtot 4
5 opls_405 5 Na Na 5
1 35.4530 ; qtot 5
6 opls_405 6 Na Na 6
1 35.4530 ; qtot 6
7 opls_405 7 Na Na 7
1 35.4530 ; qtot 7
8 opls_405 8 Na Na 8
1 35.4530 ; qtot 8
9 opls_405 9 Na Na 9
1 35.4530 ; qtot 9
.............
.............
.............
ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
When i run grompp command to prepare bilater-ions.tpr
file, I couldn't observe any error message and shown
below.
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
processing topology...
Generated 345696 of the 345696 non-bonded parameter
combinations
Generating 1-4 interactions: fudge = 0.5
Generated 345606 of the 345696 1-4 parameter
combinations
Excluding 3 bonded neighbours for POPE 96
turning all bonds into constraints...
Excluding 3 bonded neighbours for DPOP 32
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 3909
turning all bonds into constraints...
Excluding 1 bonded neighbours for NA+ 1
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at
303 K
renumbering atomtypes...
converting bonded parameters...
# ANGLES: 7520
# PDIHS: 3424
# RBDIHS: 2944
# IDIHS: 544
# LJ14: 3680
# CONSTR: 6560
# SETTLE: 3909
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Making dummy/rest group for Acceleration containing
18447 elements
Making dummy/rest group for Freeze containing 18447
elements
Making dummy/rest group for Energy Mon. containing
18447 elements
Making dummy/rest group for VCM containing 18447
elements
Number of degrees of freedom in T-Coupling group POP
is 10079.18
Number of degrees of freedom in T-Coupling group DPO
is 3423.72
Number of degrees of freedom in T-Coupling group SOL
is 23452.10
Number of degrees of freedom in T-Coupling group NA+
is 95.99
Making dummy/rest group for User1 containing 18447
elements
Making dummy/rest group for User2 containing 18447
elements
Making dummy/rest group for XTC containing 18447
elements
Making dummy/rest group for Or. Res. Fit containing
18447 elements
Making dummy/rest group for QMMM containing 18447
elements
T-Coupling has 4 element(s): POP DPO SOL NA+
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...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 65x65x70, spacing 0.119 0.119
0.117
writing run input file...
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
When I am runing mdrun command, I got the fallowing
error messages and after some time segmentation fault.
zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
Step 32, time 0.064 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.002582 (between atoms 5262 and 5310) rms
0.000038
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint
length
5262 5310 31.2 0.1000 0.0997 0.1000
Step 33, time 0.066 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.003343 (between atoms 5262 and 5310) rms
0.000057
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint
length
5368 5416 69.4 0.0999 0.1001 0.1000
Step 34, time 0.068 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.005428 (between atoms 5262 and 5310) rms
0.000076
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint
length
5262 5310 67.9 0.1003 0.0995 0.1000
5368 5416 47.0 0.1001 0.1002 0.1000
Step 35, time 0.07 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.002371 (between atoms 5368 and 5416) rms
0.000036
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint
length
5262 5310 43.4 0.0995 0.1002 0.1000
5368 5416 40.9 0.1002 0.0998 0.1000
zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
Can you tell where I have done mistake.
Any suggestion is appreciated.
Thank you in advance.
with best regards,
Nagaraju
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