[gmx-users] Questions regarding Polarization Energy Calculation
jesmin jahan
shraban03 at gmail.com
Sat Aug 18 05:23:46 CEST 2012
Okay thanks. I got it. :-)
Best Regards,
Jesmin
On Fri, Aug 17, 2012 at 11:17 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 18/08/12, *jesmin jahan * <shraban03 at gmail.com> wrote:
>>
>> Hi Mark,
>>
>> Thanks for your reply.
>>
>> In the ffnonbonded.itp, I set all sigma and epsilon values to zero.
>> So, the the LJ energy is coming as zero. But the coulomb potential is
>> non zero. What should I do to make it zero?
>
>
> Each charge-charge interaction contributes both a Coulomb term and a GB
> polarization term. They're computed at nearly the same time, because both
> need the distance, so both contribute to the same timing stats. They show up
> in the different energy terms that you see. There's no way to separate them
> - and any code that can do so is probably still slower than GROMACS doing
> both.
>
>
>> Energies (kJ/mol)
>> GB Polarization LJ (SR) Coulomb (SR) Potential Kinetic En.
>> -2.23121e+03 0.00000e+00 -3.47729e+04 -3.70041e+04 0.00000e+00
>> Total Energy Temperature Pressure (bar)
>> -3.70041e+04 0.00000e+00 0.00000e+00
>>
>>
>> One more point: I am not sure whether getting the 0 for an energy
>> does mean that it is not being calculated at all!
>
>
> Most of GROMACS is supposed to avoid computing zero interactions. It's not
> true for the all-vs-all GB loops, which you're not using, and currently not
> true for bonded interactions. Since nobody seems likely would compute
> without LJ in a real calculation, this is not a big deal from GROMACS point
> of view. I'm still skeptical about what you're trying to measure.
> Performance of well-written code is generally not additive from its
> components. If you're later going to be computing on a real molecular
> system, you're going to have LJ and/or bonded terms, and how well the codes
> compute them *together with the Coulomb terms* is what you really want to
> measure. It's like measuring how long a top chef takes to prepare a meal,
> and then wondering how they manage to feed a whole restaurant on time. They
> do lots of time-slicing and get lots of efficiencies of scale that are not
> available if you're doing just one meal.
>
>
>> It seems, the energy value was calculated but the result was zero
>> because the sigma and epsilon were zero. In that case, the time
>
>
> ...or that the LJ component of the energy is always present even if there
> are no interactions to compute for it, which I expect is the case.
>
>
>> reported by the program will also include the time of the extra
>> calculation (unless the program is smart enough to know before hand
>> that the result is going to be zero and return from the top!).
>
>
> IIRC neighbour searching detects there's no LJ and so doesn't trigger loops
> that compute LJ.
>
>
>> So,
>> while comparing with other molecular dynamic packages, its not fair to
>> report that time for gromacs which also includes non GB time (as that
>> can make Gromacs slower than others who do not include non GB-time).
>>
>> Any suggestions about this? What is the fair approach for gromacs?
>
>
> Look at the flop break-down to see if GROMACS thinks it is computing LJ any
> more. Or do some real timing measurements and compare before and after.
>
> Mark
>
>
>>
>>
>> Thanks,
>> Jesmin
>>
>> On Fri, Aug 17, 2012 at 12:00 AM, Mark Abraham <Mark.Abraham at anu.edu.au>
>> wrote:
>> > On 17/08/2012 1:14 PM, jesmin jahan wrote:
>> >>
>> >> Hi Mark,
>> >>
>> >> According to your advice " remove the the bonded terms and zero the
>> >> VDW parameters",
>> >> I removed everything under [ bond] , [angles], [pairs] and [ dihedrals
>> >> ],
>> >
>> >
>> > This only removes the "bonded" terms (in the sense of those atoms that
>> > interact because of the presence of bonds). The VDW parameters for
>> > non-bonded interactions are in ffnonbonded.itp for your force field. You
>> > should probably follow the advice here
>> >
>> > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Modifying_a_force_field
>> > to get a local copy you can change conveniently.
>> >
>> >
>> >> and run the simulation mdrun rerun.
>> >>
>> >> I got output something like the following:
>> >>
>> >>
>> >> Energies (kJ/mol)
>> >> GB Polarization LJ (SR) Coulomb (SR) Potential Kinetic
>> >> En.
>> >> -2.23121e+03 7.54287e+07 -3.47729e+04 7.53917e+07
>> >> 0.00000e+00
>> >> Total Energy Temperature Pressure (bar)
>> >> 7.53917e+07 0.00000e+00 0.00000e+00
>> >>
>> >> where the previous output was something like this:
>> >>
>> >> Energies (kJ/mol)
>> >> Bond Angle Proper Dih. Improper Dih.GB
>> >> Polarization
>> >> 2.12480e+03 4.80088e+02 1.06648e+03 9.04861e+01
>> >> -2.23122e+03
>> >> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR)
>> >> Potential
>> >> 7.05695e+02 5.47366e+03 -4.16856e+02 -8.74797e+03
>> >> -1.45483e+03
>> >> Kinetic En. Total Energy Temperature Pressure (bar)
>> >> 0.00000e+00 -1.45483e+03 0.00000e+00 0.00000e+00
>> >>
>> >>
>> >>
>> >> Energies (kJ/mol)
>> >> GB Polarization LJ (SR) Coulomb (SR) Potential Kinetic
>> >> En.
>> >> -2.23121e+03 4.17621e+13 -3.47729e+04 4.17621e+13
>> >> 0.00000e+00
>> >> Total Energy Temperature Pressure (bar)
>> >> 4.17621e+13 0.00000e+00 0.00000e+00
>> >>
>> >>
>> >> So, you can see, although it has managed to remove some extra terms,
>> >> the LJ and Columb potential are still there. I searched for VWD
>> >> parameters. Although I saw various options for VWD, its not clear
>> >> from the options, how to turn it off. Could you kindly tell me more
>> >> clearly about it?
>> >>
>> >>
>> >> I was also looking into the forcefield.itp file. I set the gen-pairs
>> >> to no , fudgeLJ 1 and fudgeQQ to 1 which were yes, .5 and .83
>> >> respectively originally.
>> >>
>> >> [ defaults ]
>> >> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>> >> 1 2 no 1 1
>> >>
>> >> Please let me know how to get rid of calculation of other energies
>> >> (LJ, Culumb and Total Potential) and how to set the parameters for
>> >> this properly.
>> >
>> >
>> > You can't get rid of the total. It's the total. You're trying to keep
>> > the
>> > (GB) Coulomb.
>> >
>> > Mark
>> >
>> >
>> >>
>> >> Thanks for your help.
>> >>
>> >> Sincerely,
>> >> Jesmin
>> >> On Thu, Aug 16, 2012 at 3:27 AM, Mark Abraham <Mark.Abraham at anu.edu.au>
>> >> wrote:
>> >>>
>> >>> On 16/08/2012 5:08 PM, jesmin jahan wrote:
>> >>>>
>> >>>> Hi Mark,
>> >>>>
>> >>>> Thanks for your reply.
>> >>>> If I open the .tpr file using notepad, it seems to be a binary file.
>> >>>> Then, how to remove the the bonded terms and zero the VDW
>> >>>> parameters?
>> >>>
>> >>>
>> >>> In the .top file from which you made the .tpr. (And contributing .itp
>> >>> files)
>> >>> Parts of chapter 5 may help with this process.
>> >>>
>> >>> Mark
>> >>>
>> >>>
>> >>>> I really need to compare how fast different well known package can
>> >>>> compute GB-polarization energy and how good the energy values are?
>> >>>> That's why time is an important factor me my experiments and I
>> >>>> really
>> >>>> want to measure the time for GB energy in isolation !
>> >>>>
>> >>>> Thanks,
>> >>>> Jesmin
>> >>>>>
>> >>>>> On Thu, Aug 16, 2012 at 2:44 AM, Mark Abraham
>> >>>>> <Mark.Abraham at anu.edu.au>
>> >>>>> wrote:
>> >>>>>>
>> >>>>>> On 16/08/2012 4:26 PM, jesmin jahan wrote:
>> >>>>>>>
>> >>>>>>> Hi Mark,
>> >>>>>>>
>> >>>>>>> Thanks for your previous reply.
>> >>>>>>> I tried to run single point energy simulation with some proteins.
>> >>>>>>> I got .log files with content like this:
>> >>>>>>>
>> >>>>>>> Energies (kJ/mol)
>> >>>>>>> Bond Angle Proper Dih. Improper Dih.GB
>> >>>>>>> Polarization
>> >>>>>>> 1.54109e+04 3.84351e+03 8.47152e+03 3.58425e+02
>> >>>>>>> -1.69666e+04
>> >>>>>>> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR)
>> >>>>>>> Potential
>> >>>>>>> 4.29664e+03 3.63997e+04 2.22900e+05 -5.18818e+04
>> >>>>>>> 2.22832e+05
>> >>>>>>> Kinetic En. Total Energy Temperature Pressure (bar)
>> >>>>>>> 1.08443e+09 1.08465e+09 2.73602e+07 0.00000e+00
>> >>>>>>> .......
>> >>>>>>>
>> >>>>>>> Computing: M-Number M-Flops %
>> >>>>>>> Flops
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> -----------------------------------------------------------------------------
>> >>>>>>> Generalized Born Coulomb 0.005711
>> >>>>>>> 0.274
>> >>>>>>> 0.2
>> >>>>>>> GB Coulomb + LJ 0.416308
>> >>>>>>> 25.395
>> >>>>>>> 18.5
>> >>>>>>> Outer nonbonded loop 0.016367
>> >>>>>>> 0.164
>> >>>>>>> 0.1
>> >>>>>>> 1,4 nonbonded interactions 0.008410
>> >>>>>>> 0.757
>> >>>>>>> 0.6
>> >>>>>>> Born radii (HCT/OBC) 0.439486
>> >>>>>>> 80.426
>> >>>>>>> 58.5
>> >>>>>>> Born force chain rule 0.439486
>> >>>>>>> 6.592
>> >>>>>>> 4.8
>> >>>>>>> NS-Pairs 0.943653 19.817
>> >>>>>>> 14.4
>> >>>>>>> Reset In Box 0.003179
>> >>>>>>> 0.010
>> >>>>>>> 0.0
>> >>>>>>> CG-CoM 0.006358 0.019
>> >>>>>>> 0.0
>> >>>>>>> Bonds 0.003219 0.190
>> >>>>>>> 0.1
>> >>>>>>> Angles 0.005838 0.981
>> >>>>>>> 0.7
>> >>>>>>> Propers 0.011273 2.582
>> >>>>>>> 1.9
>> >>>>>>> Virial 0.003899 0.070
>> >>>>>>> 0.1
>> >>>>>>> Stop-CM 0.003179 0.032
>> >>>>>>> 0.0
>> >>>>>>> Calc-Ekin 0.006358 0.172
>> >>>>>>> 0.1
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> -----------------------------------------------------------------------------
>> >>>>>>> Total 137.479
>> >>>>>>> 100.0
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> -----------------------------------------------------------------------------
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> D O M A I N D E C O M P O S I T I O N S T A T I S T I C
>> >>>>>>> S
>> >>>>>>>
>> >>>>>>> av. #atoms communicated per step for force: 2 x 6859.0
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> R E A L C Y C L E A N D T I M E A C C O U N T I N
>> >>>>>>> G
>> >>>>>>>
>> >>>>>>> Computing: Nodes Number G-Cycles Seconds %
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> -----------------------------------------------------------------------
>> >>>>>>> Domain decomp. 16 1 0.043 0.0
>> >>>>>>> 1.4
>> >>>>>>> Comm. coord. 16 1 0.003 0.0
>> >>>>>>> 0.1
>> >>>>>>> Neighbor search 16 1 0.103 0.0
>> >>>>>>> 3.5
>> >>>>>>> Force 16 1 1.530 0.5
>> >>>>>>> 51.5
>> >>>>>>> Wait + Comm. F 16 1 0.264 0.1
>> >>>>>>> 8.9
>> >>>>>>> Write traj. 16 1 0.062 0.0
>> >>>>>>> 2.1
>> >>>>>>> Update 16 1 0.001 0.0
>> >>>>>>> 0.0
>> >>>>>>> Comm. energies 16 2 0.933 0.3
>> >>>>>>> 31.4
>> >>>>>>> Rest 16 0.031 0.0
>> >>>>>>> 1.1
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> -----------------------------------------------------------------------
>> >>>>>>> Total 16 2.970 0.9
>> >>>>>>> 100.0
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> -----------------------------------------------------------------------
>> >>>>>>>
>> >>>>>>> NOTE: 31 % of the run time was spent communicating energies,
>> >>>>>>> you might want to use the -gcom option of mdrun
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> Parallel run - timing based on wallclock.
>> >>>>>>>
>> >>>>>>> NODE (s) Real (s) (%)
>> >>>>>>> Time: 0.056 0.056 100.0
>> >>>>>>> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
>> >>>>>>> Performance: 7.497 2.442 1.535 15.637
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> >From the log file, it seems, the time includes the time for LJ
>> >>>>>>> and
>> >>>>>>> Columb Potential Energy. But as I said before, I am only
>> >>>>>>> interested
>> >>>>>>> to
>> >>>>>>> GB-energy times. I am doing a comparative study of GB-energy
>> >>>>>>> performance (values vs time) for different molecular dynamic
>> >>>>>>> packages.
>> >>>>>>
>> >>>>>>
>> >>>>>> Since the LJ calculation also needs the distances, GROMACS does
>> >>>>>> them
>> >>>>>> in
>> >>>>>> the same loops and makes no apology for being efficient. :-) If
>> >>>>>> you're
>> >>>>>> really trying to measure the time for the GB energy in isolation,
>> >>>>>> then
>> >>>>>> you
>> >>>>>> will need to construct a different model physics that lacks LJ
>> >>>>>> interactions.
>> >>>>>> Or perhaps you don't really want to measure the time for GB energy
>> >>>>>> in
>> >>>>>> isolation. Depends what you're planning on using the information
>> >>>>>> for,
>> >>>>>> but
>> >>>>>> usually measuring a time representative of the calculation you plan
>> >>>>>> to
>> >>>>>> run
>> >>>>>> later is a good way to avoid having to account for lots of
>> >>>>>> subtleties
>> >>>>>> of
>> >>>>>> different packages.
>> >>>>>>
>> >>>>>>
>> >>>>>>> That's why I was trying to deduct the time for any other extra
>> >>>>>>> energy
>> >>>>>>> computation time from it.
>> >>>>>>>
>> >>>>>>> Can anyone tell me how to get the exact time of GB-polarization
>> >>>>>>> energy
>> >>>>>>> (including Born radii) and excluding the times for any other
>> >>>>>>> additional energy (like LJ and Columb etc) from gromacs
>> >>>>>>> simutation?
>> >>>>>>
>> >>>>>>
>> >>>>>> The .tpr you use for the rerun doesn't have to be one that will
>> >>>>>> produce
>> >>>>>> a sensible model physics. If you remove the bonded terms and zero
>> >>>>>> the
>> >>>>>> VDW
>> >>>>>> parameters then the only thing left to compute is the
>> >>>>>> electrostatics,
>> >>>>>> which
>> >>>>>> will give you the time you seek. You'll still potentially have time
>> >>>>>> spent
>> >>>>>> doing neighbour searching, and that is something you need to
>> >>>>>> consider
>> >>>>>> for
>> >>>>>> gauging relative performance of different packages. Again, the
>> >>>>>> times
>> >>>>>> you
>> >>>>>> measure will not be significant unless you run for at least several
>> >>>>>> minutes.
>> >>>>>>
>> >>>>>> Mark
>> >>>>>>
>> >>>>>>
>> >>>>>>> Thanks,
>> >>>>>>> Jesmin
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> On Tue, Aug 14, 2012 at 10:16 AM, jesmin jahan
>> >>>>>>> <shraban03 at gmail.com>
>> >>>>>>> wrote:
>> >>>>>>>>
>> >>>>>>>> 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
>> >>>>>>>>> --
>> >>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>> >>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>>>>>>>> * Only plain text messages are allowed!
>> >>>>>>>>> * Please search the archive at
>> >>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before
>> >>>>>>>>> posting!
>> >>>>>>>>> * Please don't post (un)subscribe requests to the list. Use the
>> >>>>>>>>> www
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>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>> --
>> >>>>>>>> Jesmin Jahan Tithi
>> >>>>>>>> PhD Student, CS
>> >>>>>>>> Stony Brook University, NY-11790.
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>> --
>> >>>>>> gmx-users mailing list gmx-users at gromacs.org
>> >>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>>>>> * Only plain text messages are allowed!
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>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> --
>> >>>>> Jesmin Jahan Tithi
>> >>>>> PhD Student, CS
>> >>>>> Stony Brook University, NY-11790.
>> >>>>>
>> >>>>
>> >>>> --
>> >>>> Jesmin Jahan Tithi
>> >>>> PhD Student, CS
>> >>>> Stony Brook University, NY-11790.
>> >>>
>> >>>
>> >>> --
>> >>> gmx-users mailing list gmx-users at gromacs.org
>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>> * Only plain text messages are allowed!
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>> >>
>> >>
>> >>
>> >
>> > --
>> > gmx-users mailing list gmx-users at gromacs.org
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>>
>>
>> --
>> Jesmin Jahan Tithi
>> PhD Student, CS
>> Stony Brook University, NY-11790.
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
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