[gmx-users] destruction of the structure of a molecule in water after energy minimization

[Saeed Nasiri]

Dear all

I created the topology and itp files for a molecule manually (the
parameters are not exist in the usual force fields) and build a box of a
molecule and 857 water molecules. The structure of the molecule in water
box is OK. Then the energy minimization step was done by the following
files. After the successful termination, the structure of the molecule has
been destroyed and the atoms of the molecule are spread in the box. In the
following the employed files and the structure of the molecule (in gro
format) before and after minimization (without water molecule) are
presented.
 Any help will highly appreciated.

####################### before minimization ###############################
    1BM    CW    1   1.222   1.373   1.397
    1BM    CW    2   1.349   1.331   1.419
    1BM    CR    3   1.308   1.498   1.557
    1BM   HCW    4   1.148   1.339   1.327
    1BM   HCW    5   1.408   1.254   1.371
    1BM   HCR    6   1.318   1.570   1.636
    1BM    NA    7   1.196   1.475   1.486
    1BM    NA    8   1.400   1.408   1.521
    1BM    C1    9   1.540   1.411   1.566
    1BM    H1   10   1.571   1.308   1.584
    1BM    H1   11   1.541   1.464   1.662
    1BM    C2   12   1.631   1.482   1.466
    1BM    HC   13   1.588   1.580   1.446
    1BM    HC   14   1.630   1.426   1.372
    1BM    CS   15   1.774   1.494   1.518
    1BM    HC   16   1.814   1.395   1.542
    1BM    HC   17   1.774   1.551   1.611
    1BM    CT   18   1.867   1.563   1.418
    1BM    HC   19   1.831   1.663   1.394
    1BM    HC   20   1.969   1.572   1.458
    1BM    HC   21   1.873   1.507   1.324
    1BM    C1   22   1.082   1.566   1.484
    1BM    H1   23   1.032   1.567   1.581
    1BM    H1   24   1.011   1.532   1.409
    1BM    H1   25   1.121   1.665   1.461
    2Cl      Cl   26   2.283   1.962   0.221

#################### after minimization ###################################
    1BM    CW    1   1.030   1.807   0.330
    1BM    CW    2   1.253   0.613   1.483
    1BM    CR    3   0.962   1.561   1.355
    1BM   HCW    4   0.754   0.906   0.667
    1BM   HCW    5   1.875   0.398   0.729
    1BM   HCR    6   0.982   2.417   2.358
    1BM    NA    7   0.291   0.861   1.603
    1BM    NA    8   0.845   0.979   2.444
    1BM    C1    9   1.834   0.830   2.413
    1BM    H1   10   1.844   0.003   1.938
    1BM    H1   11   1.443   1.743   2.290
    1BM    C2   12   1.917   1.355   1.566
    1BM    HC   13   1.404   2.327   1.676
    1BM    HC   14   1.558   1.096   0.699
    1BM    CS   15   2.661   1.364   2.237
    1BM    HC   16   2.317   0.518   1.479
    1BM    HC   17   2.099   2.175   2.002
    1BM    CT   18   2.036   1.892   0.626
    1BM    HC   19   2.109   2.565   1.277
    1BM    HC   20   2.648   1.892   1.400
    1BM    HC   21   2.494   1.027   0.829
    1BM    C1   22   0.417   2.454   1.333
    1BM    H1   23   0.484   1.849   2.126
    1BM    H1   24   0.182   1.535   0.847
    1BM    H1   25   1.280   2.539   0.925
    2Cl      Cl   26   2.580   2.241   2.823

################# minimum.mdp ############################
; minim.mdp - used as input into grompp to generate em.tpr

integrator    = steep        ; Algorithm (steep = steepest descent
minimization)
emtol        = 10.0      ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps        = 500000      ; Maximum number of (minimization) steps to
perform
define         = -DFLEXIBLE

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist               = 1            ; Frequency to update the neighbor
list and long range forces
cutoff-scheme       = Verlet
ns_type                = grid        ; Method to determine neighbor list
(simple, grid)
coulombtype            = PME        ; Treatment of long range electrostatic
interactions
rcoulomb            = 1.0        ; Short-range electrostatic cut-off
rvdw                = 1.0        ; Short-range Van der Waals cut-off
pbc                = xyz         ; Periodic Boundary Conditions (yes/no)

########################## topol.top
########################################

#include "oplsaa.ff/forcefield.itp"


#include "ff_BM.itp"
#include "BM.itp"
#include "Cl.itp"

; Include water topology
#include "oplsaa.ff/tip3p.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

[system]
BM Cl

[molecules]
BM        1
Cl          1
SOL               857