[gmx-users] Re:mdrun_problem

[pkmukher]

Mark and other users,

  Thanks for the input. I understand that translation does
not have any effect on the energy calculations since the
point of reference is the protein itself.
The problem over here is that if a translation operation is
to be done it should perform the same operation on all the
X,Y or Z coordinates. 
  A brief summary of the job - i have a protein + peptide
system which i want to simulate. I have generated peptide
itp file using PRODRG and included in the protein .top
file. I am doing a dummy mdrun to check the system.
I have added excerpts from the structure files and the .mdp
file.The first is the input structure file for grompp > .trp
file > mdrun while the second is the output of the
mdrun.Comparing the two structures whats happening is that
for the protein coordinates (till 1895) a tranlation is
being performed only on the protein X coordinates while for
the peptide the translation is being performed only on the Y
and Z coordinates. This results in the peptide and protein
to be placed separate from each other.Please help me with
your suggestions. Thanks in advance

####
input structure
####

ATOM   1890  CD2 HIS A 181      17.104 -17.966  35.020  1.00
 0.00
ATOM   1891  CE1 HIS A 181      15.979 -16.114  34.942  1.00
 0.00
ATOM   1892  NE2 HIS A 181      17.022 -16.732  34.381  1.00
 0.00
ATOM   1893  C   HIS A 181      15.328 -21.621  37.119  1.00
 0.00
ATOM   1894  O1  HIS A 181      14.341 -22.372  36.561  1.00
 0.00
ATOM   1895  O2  HIS A 181      15.818 -21.755  38.381  1.00
 0.00
TER
HETATM    1  NAA DRG   182       3.259 -11.741 -15.248  1.00
20.00
HETATM    2  HAA DRG   182       2.868 -11.170 -15.970  1.00
20.00
HETATM    3  HAB DRG   182       4.140 -12.104 -15.551  1.00
20.00
HETATM    4  HAC DRG   182       2.637 -12.498 -15.050  1.00
20.00
HETATM    5  CAB DRG   182       3.456 -10.923 -14.017  1.00
20.00
HETATM    6  CAC DRG   182       4.054 -11.797 -12.913  1.00
20.00
HETATM    7  OAD DRG   182       3.478 -12.789 -12.512  1.00
20.00
HETATM    8  N   DRG   182       5.208 -11.438 -12.418  1.00
20.00
HETATM    9  HAD DRG   182       5.666 -10.619 -12.763  1.00
20.00
HETATM   10  CA  DRG   182       5.843 -12.248 -11.340  1.00
20.00

####
output structure
####

ATOM   1890  CD2 HIS A 181      57.476 -17.958  35.022  1.00
 0.00
ATOM   1891  CE1 HIS A 181      56.353 -16.113  34.945  1.00
 0.00
ATOM   1892  NE2 HIS A 181      57.395 -16.742  34.389  1.00
 0.00
ATOM   1893  C   HIS A 181      55.696 -21.634  37.130  1.00
 0.00
ATOM   1894  O1  HIS A 181      54.730 -22.362  36.575  1.00
 0.00
ATOM   1895  O2  HIS A 181      56.185 -21.754  38.363  1.00
 0.00
ATOM   1896  NAA DRG B 182       3.259  41.631  44.612  1.00
 0.00
ATOM   1897  HAA DRG B 182       2.868  42.201  43.887  1.00
 0.00
ATOM   1898  HAB DRG B 182       4.140  41.267  44.306  1.00
 0.00
ATOM   1899  HAC DRG B 182       2.637  40.873  44.807  1.00
 0.00
ATOM   1900  CAB DRG B 182       3.456  42.447  45.837  1.00
 0.00
ATOM   1901  CAC DRG B 182       4.052  41.573  46.943  1.00
 0.00
ATOM   1902  OAD DRG B 182       3.475  40.579  47.344  1.00
 0.00
ATOM   1903  N   DRG B 182       5.210  41.933  47.440  1.00
 0.00
ATOM   1904  HAD DRG B 182       5.668  42.752  47.095  1.00
 0.00
ATOM   1905  CA  DRG B 182       5.844  41.127  48.515  1.00
 0.00


####
.mdp file
####

cpp             = /usr/bin/cpp
constraints     = none
integrator      = cg
nsteps          = 1
emtol           = 100.0
emstep          = 0.01
nstcomm         =1
ns_type         = grid
morse           = no ; was given as yes in tutorial
coulombtype     = shift
vdw_type        = shift
rlist           = 1.4
rcoulomb        = 1.2
rvdw            = 1.2
rcoulomb_switch = 1.0
rvdw_switch     = 1.0
epsilon_r       = 6.0


Prasenjit Kumar Mukherjee
Graduate Student
Department of Medicinal Chemistry
School of Pharmacy
University of Mississippi
USA

Cell   - 662 380 0146
Office - 662 915 1286