[gmx-users] to gro or not to gro

[David van der Spoel]

On 2011-11-26 16:38, Igor Druz wrote:
> 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 pdb has more decimal digits, hence you have two "different" sets of 
coordinates.
If you convert the gro back to pdb and the redo the procedure you should 
get identical numbers.

> 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 <http://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?
>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se