[gmx-users] Questions regarding Polarization Energy Calculation

jesmin jahan shraban03 at gmail.com
Mon Aug 13 23:38:39 CEST 2012

Dear Gromacs Users,

I have some questions regarding GB-Polarization Energy Calculation
with Gromacs. I will be grateful if someone can help me with the

I am trying to calculate GB-Polarization energy for different Protein
molecules. I am interested both in energy values with the time
required to calculate the Born Radii and Polarization Energy.
I am not doing any energy minimization step as the files I am using as
input are already minimized.

Here is the content of my  mdrun.mdp file:

constraints         =  none
integrator            =  md
pbc                       =  no
dt                         =  0.001
nsteps                 =  0
implicit_solvent    =  GBSA
gb_algorithm        =  HCT
sa_algorithm        =  None

And I am using following three steps for all the .pdb files I have:

let x is the name of the .pdb file.

pdb2gmx -f x.pdb -ter -ignh -ff amber99sb -water none
grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr
mpirun -np 8 mdrun_mpi  -deffnm imd -v -g x.log

1 .Now the running time reported by a log file also includes other
times. Its also not clear to me whether the time includes the time for
Born Radii calculations.
So, to get the GB-energy time  I am doing the following: I am also
running a simulation with "implicit_solvent" set to "no" and I am
taking the difference of these two (with GB and Without GB). Is that a
right approach?
I also want to be sure that it also includes Born-Radii calculation time.

Is there any other approach to do this?

2. I was trying to run the simulations on 192 cores (16 nodes each
with 12 codes). But I got "There is no domain decomposition for 12
nodes that is compatible with the given box and a minimum cell size of
2.90226 nm" error for some pdb files. Can anyone explain what is
happening. Is there any restriction on number of nodes can be used?

3. I run the simulations with 1 way 96 (8 nodes each with 12 cores).
Its not clear to me from the log file whether Gromacs is able to
utilize all the 92 cores. It seems, it is using only 8 nodes.
Does Gromacs use both shared and distributed memory parallelism?

4.   In the single-point energy  calculation "mdrun -s input.tpr
-rerun configuration.pdb", is the configuration.pdb mentioned  is the
original pdb file used on pdb2gmx  with -f option? Or its a modified
pdb file? I am asking because if I use the original file that does not
work always :-(

5. Is there any known speedup factor of Gromacs on multicores?

Thanks for your help.

Best Regards,

Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.

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