[gmx-users] distance restraint in gromacs md run

[Simon Kit Sang Chu]

Hi,

I have a protein of interest which requires distance restraint for C alpha
atoms. However, the simulation does not seem to include the restraint at
all.

*prod.mdp*
define              = -DPOSRES
constraints         =  none
integrator          =  md
dt                  =  0.005
nsteps              =  40000000         ; 200 ns



*p1p2-merged.top*

; Include forcefield parameters
#include "ffPACE_1.3.itp"

[ moleculetype ]
; Name            nrexcl
Protein_A         3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
   chargeB      massB
     1         N+      1    MET      N      1        0.7         17   ;
qtot 0.7
.
.
.
 1861  1862  1863  1864     1

; Include distance restraint file
#ifdef POSRES
#include "p1p2_dist.itp"
#endif

*p1p2_dist.itp*
; distance restraints for r_1-62_r_115-176_&_C-alpha of FullP1P2 in water

[ distance_restraints ]
;   i     j ? label      funct         lo        up1        up2     weight
    2    11 1     0          1   0.283898   0.483898     1.4839          1
    2    17 1     1          1   0.552993   0.752993    1.75299          1
.
.
.

 Do I need to use "define = -DDISTRES" and "ifdef DISPOSRES" instead? Is
distance restraint only used in NMR refinement but not MD?

Thanks in advance,
Simon