[gmx-users] mdrun_problem

[pkmukher]

Hello users,

  I am trying to check wether my prepared system is ready to
be put into a simualtion. I have a 2 body system 1protein +
1peptide. I have prepared the peptide using PRODRG server
and included it into the protein .top file. I wanted to do a
dummy minimization run with my prepared protein using 1step
of CG. I am noticing that the protein portion (not the
peptide/ligand) undergoes a shift in the X coordinate only
between the input and output structures. All of the X
coordinates are shifted by 40.37 units.
e.g. 1 -18.608  to  21.767. I have used an mdp file from a
tutorial.

following is the .mdp file and excerpts from the input and
output structure files. Could you please give me your
suggestions as to what is possibly happening here.Thanks in
advance..Prasenjit

####
.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
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

 
####
input structure file excerpt
####

ATOM      1  N   MET A   1     -18.608   9.660  16.832  1.00
 0.00
ATOM      2  H1  MET A   1     -19.259   9.669  17.591  1.00
 0.00
ATOM      3  H2  MET A   1     -19.007  10.131  16.045  1.00
 0.00
ATOM      4  H3  MET A   1     -18.399   8.714  16.583  1.00
 0.00
ATOM      5  CA  MET A   1     -17.356  10.354  17.244  1.00
 0.00
ATOM      6  CB  MET A   1     -16.746   9.633  18.448  1.00
 0.00
ATOM      7  CG  MET A   1     -17.079  10.403  19.728  1.00
 0.00
ATOM      8  SD  MET A   1     -16.154  11.959  19.754  1.00
 0.00
ATOM      9  CE  MET A   1     -17.575  13.069  19.606  1.00
 0.00
ATOM     10  C   MET A   1     -16.359  10.341  16.082  1.00
 0.00
ATOM     11  O   MET A   1     -15.160  10.335  16.280  1.00
 0.00
ATOM     12  N   SER A   2     -16.845  10.337  14.871  1.00
 0.00
ATOM     13  H   SER A   2     -17.835  10.343  14.729  1.00
 0.00
ATOM     14  CA  SER A   2     -15.924  10.324  13.699  1.00
 0.00


####
output structure file excerpt
####

ATOM      1  N   MET A   1      21.767   9.661  16.834  1.00
 0.00
ATOM      2  H1  MET A   1      21.115   9.669  17.591  1.00
 0.00
ATOM      3  H2  MET A   1      21.367  10.131  16.045  1.00
 0.00
ATOM      4  H3  MET A   1      21.975   8.714  16.583  1.00
 0.00
ATOM      5  CA  MET A   1      23.016  10.351  17.241  1.00
 0.00
ATOM      6  CB  MET A   1      23.626   9.633  18.449  1.00
 0.00
ATOM      7  CG  MET A   1      23.295  10.400  19.728  1.00
 0.00
ATOM      8  SD  MET A   1      24.217  11.965  19.755  1.00
 0.00
ATOM      9  CE  MET A   1      22.803  13.067  19.607  1.00
 0.00
ATOM     10  C   MET A   1      24.015  10.341  16.085  1.00
 0.00
ATOM     11  O   MET A   1      25.218  10.335  16.282  1.00
 0.00
ATOM     12  N   SER A   2      23.529  10.337  14.867  1.00
 0.00
ATOM     13  H   SER A   2      22.540  10.343  14.726  1.00
 0.00
ATOM     14  CA  SER A   2      24.447  10.323  13.699  1.00
 0.00

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

Cell   - 662 380 0146
Office - 662 915 1286