[gmx-users] Questions regarding Polarization Energy Calculation

[jesmin jahan]

Thanks Mark for your reply. I was trying to use Single-Point Energy
Calculation as you advised in your first reply but for most of the
files the simulation failed because I was using the original .pdb
files in the mdrun command.

Anyways. I really appreciate your help.
Thanks again,
Jesmin

On Tue, Aug 14, 2012 at 1:26 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 14/08/2012 7:38 AM, jesmin jahan wrote:
>>
>> 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
>> answers.
>>
>> 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
>
>
> So you're not using the advice I gave you about how to calculate single
> point energies. OK.
>
>
>> 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.
>
>
> The timing breakdown is printed at the end of the .log file. Likely your
> time is heavily dominated by the GB calculation and communication cost. Born
> radii calculation are part of the former, and not reported separately. You
> should not bother with timing measurements unless your run goes for at least
> several minutes, else your time will be dominated by I/O and setup costs.
>
>
>> 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?
>
>
> No, that measures the weight difference between an apple and an orange, not
> whether the apple's seeds are heavy.
>
>
>> I also want to be sure that it also includes Born-Radii calculation time.
>
>
> It's part of the GB calculation, so it's included in its timing.
>
>
>>
>> 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?
>
>
> Yes. See discussion linked from http://www.gromacs.org/Documentation/Errors
>
>
>>
>> 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?
>
>
> Not at the moment. Look at the top of your .log file for clues about what
> your configuration is making available to GROMACS. It is likely that mpirun
> -np 8 makes only 8 MPI processes available to GROMACS. Using more will
> require you to use your MPI installation correctly (and we can't help with
> that).
>
>
>> 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 :-(
>
>
> It can be any configuration that matches the .top file you gave to grompp.
> That's the point - you only need one run input file to compute the energy of
> any such configuration you later want. The configuration you gave to grompp
> (or any other tool) doesn't matter.
>
>
>> 5. Is there any known speedup factor of Gromacs on multicores?
>
>
> That depends on your simulation system, hardware, network and algorithm.
> Don't bother with fewer than hundreds of atoms per core.
>
> Mark
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-- 
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.