[gmx-users] Re: constraints using all-angles
Sang-Won Park
icocoon1 at gmail.com
Mon May 17 07:31:50 CEST 2010
I omitted mass of fluorine atoms, while I typed. It's 18.9984.
So, the topology file is as follows.
[ 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 18.9984
3 F2 1 PF6 F2 1 -0.39 18.9984
4 F3 1 PF6 F3 1 -0.39 18.9984
5 F4 1 PF6 F4 1 -0.39 18.9984
6 F5 1 PF6 F5 1 -0.39 18.9984
7 F6 1 PF6 F6 1 -0.39 18.9984
And the other things are the same.
On Mon, 2010-05-17 at 13:06 +0900, Sang-Won Park wrote:
> 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?
More information about the gromacs.org_gmx-users
mailing list