[gmx-users] to gro or not to gro

Igor Druz idruz512 at gmail.com
Sat Nov 26 17:37:47 CET 2011 

I already knew the reason. But I had to find this out hard way. Now facing
a dreading prospect of repeating tons of calculations!  Hence the request
for the "bad for the health" sign. Btw, gromacs issues a lot of warnings,
but not this one :D

What a bright idea to switch from angstroms to nanometers! Now the gro
files carry a lot of useless zeros.

 On Sat, Nov 26, 2011 at 3:55 PM, <chris.neale at utoronto.ca> wrote:

> There is rounding because of angstroms vs nanometers and both files
> maintain 3 decimal places (see below).
>
> The intention of pdb2gmx is not to get a .gro , but to get a .top or .itp
> file.
>
> I see your point, but I don't think it matters. If you really need that
> precision, then I'd think that you'd be using double precision gromacs
> (which would still round the output .gro from pdb2gmx and not solve this
> issue... just saying).
>
> gpc-f101n084-$ tail a.gro
>    2GLY    HA2   11  -0.426   0.215   0.193
>    2GLY      C   12  -0.446   0.390   0.072
>    2GLY      O   13  -0.368   0.440  -0.013
>    3NME      N   14  -0.532   0.478   0.154
>    3NME      H   15  -0.618   0.488   0.104
>    3NME    CH3   16  -0.468   0.607   0.173
>    3NME   HH31   17  -0.375   0.594   0.227
>    3NME   HH32   18  -0.533   0.670   0.234
>    3NME   HH33   19  -0.447   0.661   0.081
>   0.47330   0.80470   0.29640
> gpc-f101n084-$ tail a.pdb
> ATOM     11  HA2 GLY     2      -4.263   2.147   1.932
> ATOM     12  C   GLY     2      -4.461   3.901   0.720
> ATOM     13  O   GLY     2      -3.677   4.400  -0.128
> HETATM   14  N   NME     3      -5.316   4.776   1.535
> HETATM   15  H   NME     3      -6.182   4.876   1.044
> HETATM   16  CH3 NME     3      -4.685   6.072   1.731
> HETATM   17 1HH3 NME     3      -3.754   5.941   2.272
> HETATM   18 2HH3 NME     3      -5.328   6.697   2.341
> HETATM   19 3HH3 NME     3      -4.465   6.615   0.809
> END
>
> -- original message --
>
> 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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