Dear All,
In my simulation I want to fix the S=O bond length of SO2, but the
angle has to be kept flexible. So I search for the distance restraints
in gromacs mailing list and
accordingly I have incorporated the distant_restraints block in the
topology file. After a short equilibration, when I am seeing the movie
of the trajectory, the bond length is changing. So what is the right
way to keep the distance fixed and the angle flexible ?
Part of the topology file is as follows
; Include forcefield parameters
#include "./amber94ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Other_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 502 SR rtp CR q 0.0
1 S 502 SR S 1 0.6512 32.07 ;
qtot 0.6512
2 O 502 SR O1 2 -0.3256 16 ;
qtot 0.3256
3 O 502 SR O2 3 -0.3256 16 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
[ distance_restraints ]
; ai aj type index type' low up1 up2 fac
1 2 1 0 1 1.149 1.490 1.490 1.0
1 3 1 0 1 1.149 1.490 1.490 1.0
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "./amber94.ff/spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "./amber94.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Other_chain_A 1
SOL 622
--
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
JNCASR
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
