Hello,
I'm trying to do set a configuration for BMIM PF6 with rigid body anion.
So, I tested all-angles constraints for one molecule of PF6-.
Below is the conf.gro file.
-----------------------------------------------------
PF6
7
1PF6 P1 1 0.000 0.000 0.000
1PF6 F1 2 0.156 0.000 0.000
1PF6 F2 3 0.000 0.156 0.000
1PF6 F3 4 0.000 0.000 0.156
1PF6 F4 5 -0.156 0.000 0.000
1PF6 F5 6 0.000 -0.156 0.000
1PF6 F6 7 0.000 0.000 -0.156
2.50000 2.50000 2.50000
-----------------------------------------------------
And below is a part of .top file. I fix all bonds and the distances
between fluorine atoms.
-----------------------------------------------------
[ moleculetype ]
; Name nrexcl
PF6 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 P1 1 PF6 P1 1 1.34 30.9738
2 F1 1 PF6 F1 1 -0.39
3 F2 1 PF6 F2 1 -0.39
4 F3 1 PF6 F3 1 -0.39
5 F4 1 PF6 F4 1 -0.39
6 F5 1 PF6 F5 1 -0.39
7 F6 1 PF6 F6 1 -0.39
[ constraints ]
; ai aj funct b0
1 2 1 0.1560 ; bond length = 0.1560 nm
1 3 1 0.1560
1 4 1 0.1560
1 5 1 0.1560
1 6 1 0.1560
1 7 1 0.1560
2 3 2 0.22061731573 ; sqrt(2)*0.1560 nm
4 5 2 0.22061731573
6 7 2 0.22061731573
3 4 2 0.22061731573
5 6 2 0.22061731573
2 7 2 0.22061731573
2 4 2 0.22061731573
2 6 2 0.22061731573
3 5 2 0.22061731573
3 7 2 0.22061731573
4 6 2 0.22061731573
5 7 2 0.22061731573
2 5 2 0.3120 ; 2*0.1560 nm
3 6 2 0.3120
4 7 2 0.3120
------------------------------------------------------------------
After minimizing the configuration, I got the confout.gro file as
follows.
------------------------------------------------------------------
PF6
7
1PF6 P1 1 0.000 0.000 0.000
1PF6 F1 2-592.510 0.000 0.000
1PF6 F2 3 0.000-592.510 0.000
1PF6 F3 4 0.000 0.000-592.510
1PF6 F4 5 592.510 0.000 0.000
1PF6 F5 6 0.000 592.510 0.000
1PF6 F6 7 0.000 0.000 592.510
2.50000 2.50000 2.50000
------------------------------------------------------------------
When I ran a simulation with md integrator option, it shows several
messages as follows, and finally all the atoms go to infinity.
------------------------------------------------------------------
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 105.918804, max 105.972168 (between atoms 1 and 6)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 180.0 0.1560 16.6815 0.1560
1 3 180.0 0.1560 16.6710 0.1560
1 4 180.0 0.1560 16.6800 0.1560
1 5 180.0 0.1560 16.6772 0.1560
1 6 180.0 0.1560 16.6877 0.1560
1 7 180.0 0.1560 16.6787 0.1560
2 3 180.0 0.2206 23.5848 0.2206
4 5 180.0 0.2206 23.5873 0.2206
6 7 180.0 0.2206 23.5923 0.2206
3 4 180.0 0.2206 23.5840 0.2206
5 6 nan 0.2206 23.5915 0.2206
2 7 180.0 0.2206 23.5890 0.2206
2 4 180.0 0.2206 23.5897 0.2206
2 6 180.0 0.2206 23.5939 0.2206
3 5 180.0 0.2206 23.5824 0.2206
3 7 180.0 0.2206 23.5832 0.2206
4 6 180.0 0.2206 23.5931 0.2206
5 7 180.0 0.2206 23.5866 0.2206
Wrote pdb files with previous and current coordinates
------------------------------------------------------------------
What's wrong with my input files?
--
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