[gmx-users] to gro or not to gro

[Igor Druz]

There was no water. Version 4.5.5. Single precision. This is what I ran:

pdb2gmx -f 1.pdb -p g1 -o g1
grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top
mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene
Potential energy: 1.19780e+02 kJ/mol

grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top
mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene
Potential energy: 1.15997e+02 kJ/mol

The mdp file:

integrator               = md
nsteps                   = 0
nstcomm                  = 1
nstxout                  = 1
nstvout                  = 1
nstfout                  = 0
nstlog                   = 1
nstenergy                = 1
nstxtcout                = 0
nstlist                  =  0
ns_type                  = simple
pbc                      = no
rlist                    = 0
rcoulomb                 = 0
rvdw                     = 0
gen_vel                  = no
unconstrained-start      = yes
lincs-warnangle          = 30

The pdb file :

HETATM    1 1HH3 ACE     1      -1.449   0.109  -0.581
  H
HETATM    2  CH3 ACE     1      -2.101  -0.268   0.202
  C
HETATM    3 2HH3 ACE     1      -1.708   0.090   1.151
  H
HETATM    4 3HH3 ACE     1      -2.109  -1.350   0.189
  H
HETATM    5  C   ACE     1      -3.491   0.269   0.000
  C
HETATM    6  O   ACE     1      -4.453  -0.401  -0.152
  O
ATOM      7  N   GLY     2      -3.601   1.734   0.000
  N
ATOM      8  H   GLY     2      -3.039   2.278  -0.623
  H
ATOM      9  CA  GLY     2      -4.525   2.391   0.903
  C
ATOM     10  HA1 GLY     2      -5.539   2.051   0.696
  H
ATOM     11  HA2 GLY     2      -4.263   2.147   1.932
  H
ATOM     12  C   GLY     2      -4.461   3.901   0.720
  C
ATOM     13  O   GLY     2      -3.677   4.400  -0.128
  O
HETATM   14  N   NME     3      -5.316   4.776   1.535
  N
HETATM   15  H   NME     3      -6.182   4.876   1.044
  H
HETATM   16  CH3 NME     3      -4.685   6.072   1.731
  C
HETATM   17 1HH3 NME     3      -3.754   5.941   2.272
  H
HETATM   18 2HH3 NME     3      -5.328   6.697   2.341
  H
HETATM   19 3HH3 NME     3      -4.465   6.615   0.809
  H
END


*In reply to chris.neale at utoronto.ca:*

It's more useful if you provide more information. What was the .pdb

file (can I download it from the pdb databank?) was there water? what

version of gromacs? was it compiled in double or single precision?

what were your mdp parameters?
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