On 7/23/12 8:31 AM, tarak karmakar wrote:
Thanks for the reply.
But then what should I give as Kb [ bond stretching constant ] in the
ffbonded.itp file ? should I give 00.000 there or something else ???
Constraints make bonds rigid. The force constant is irrelevant.
-Justin
On Mon, Jul 23, 2012 at 4:11 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 7/23/12 2:39 AM, tarak karmakar wrote:
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 ?
Use constraints for the bonds, not distance restraints.
-Justin
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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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