[gmx-users] Re: free energy calculation , grompp crash
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 8 01:42:19 CET 2011
Da-Wei Li wrote:
> hello
>
> 1. I used almost identical comands with you.
> 2. If I set "couple-intramol = yes". My grompp will run very fast.
>
> From the manu, "couple-intramol = no means " all intramol
> (protein-protein interaction in my case) interaction are turned to
> predefind list while "couple-intramol = yes" means
> intra-protein interactions are scaled the same with protein-water
> interaction. Maybe this is the reason my grompp becomes very slow??
>
That seems likely. As I suggested before, grompp is chewing up a lot of memory
converting all intramolecular nonbonded interactions into pairs and exclusions.
This is a very intensive process, and scales with system size.
> 3. If I set "couple-intramol = yes", my mdrun will go very
> smooth. It is also fine if I turn off free energy calculation. If I set
> "couple-intramol=no", it will complain "two-body bonded interactions:
> 4.509 nm, LJC Pairs NB, atoms 1013 1231". This is very strange. Atom
> 1013 and 1231 are not bonded at all, they are actually the most *far
> away* pair in my system. I can't understand why free energy calculation
> will cause this message.
>
This is a consequence of the description above. Check the output of grompp -pp
or the .tpr file and you will likely see that interactions within your protein
are now being assigned to the [pairs] and [exclusions] directives. As a result,
you have "bonded" interactions that are very far apart. You might be able to
use mdrun -pd to circumvent this performance issue (although it will be slower
than DD in most cases, here it will likely be faster than any construct DD might
come up with, if it runs at all).
-Justin
>
> best,
>
> dawei
> On Mon, Feb 7, 2011 at 6:16 PM, TJ Mustard <mustardt at onid.orst.edu
> <mailto:mustardt at onid.orst.edu>> wrote:
>
> Da-Wei,
>
>
>
> How do you generate your box, solvent, ions?
>
>
>
> I use this sequence of commands:
>
> pdb2gmx -f protein.pdb -o protein.gro -p protein.top
> editconf -bt cubic -f protein.gro -o protein.gro -c -d 1.5
> genbox -cp protein.gro -cs spc216.gro -o protein_b4ion.gro -p
> protein.top
> grompp -f em.mdp -c protein_b4ion.gro -p protein.top -o
> protein_b4ion.tpr
> genion -s protein_b4ion.tpr -o protein_b4em.gro -neutral -conc 0.001
> -pname NA -nname CL -g protein_ion.log -p protein.top
>
> Then I will grompp and mdrun. I seldom change these values.
>
> Thank you,
> TJ Musard
>
>
>
>
> On February 7, 2011 at 1:08 PM Da-Wei Li <lidawei at gmail.com
> <mailto:lidawei at gmail.com>> wrote:
>
>> hi, all
>> I get another strange error. Once I turn on free energy
>> calculation. mdrun will complain this:
>> Initial maximum inter charge-group distances:
>> two-body bonded interactions: 4.509 nm, LJC Pairs NB, atoms
>> 1013 1231
>> multi-body bonded interactions: 0.428 nm, Proper Dih., atoms 5 13
>> Minimum cell size due to bonded interactions: 4.960 nm
>> so that domain decomposition will not work. What is a LJC pair? I
>> did not see any problem with my system. Everything is fine
>> if free_energy = no.
>> thanks.
>> dawei
>>
>> On Mon, Feb 7, 2011 at 1:38 PM, Da-Wei Li <lidawei at gmail.com
>> <mailto:lidawei at gmail.com>> wrote:
>>
>> hello
>> My goal is to study the solvation free energy of a fixed
>> protein and compare it with implicit model. The pr1. mdp is
>> just a test case. Grompp always need more than 10 minutes to
>> finish for my 76 residues protein when free_energy = yes, no
>> matter there is PR or not, whether I switch off only vdm or
>> switch both ele and vdm.
>> The memory usage is <1% on a system with 16GB memory so that
>> memory limitation can be ruled out.
>> best,
>> dawei
>>
>>
>> On Mon, Feb 7, 2011 at 1:31 PM, TJ Mustard
>> <mustardt at onid.orst.edu <mailto:mustardt at onid.orst.edu>> wrote:
>>
>> Da-Wei,
>>
>>
>> Do you need FEP information on the PR step? Are you going
>> to do a MD(sd) with FEP on after the PR?
>>
>>
>>
>> And are you doing hydration of a protein?
>>
>>
>>
>> Thank you,
>>
>> TJ Mustard
>>
>> On February 7, 2011 at 10:23 AM "Justin A. Lemkul"
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>> wrote:
>>
>> >
>> >
>> > Da-Wei Li wrote:
>> > > hello
>> > >
>> > > Here they are the command line and mdp file. I use
>> Gromacs 4.5.3. This
>> > > is a test case only and the protein is 1UBQ. Grompp
>> wills top for about
>> > > 10 minutes then go through.
>> > >
>> >
>> > The efficiency of this kind of process will depend on
>> the amount of available
>> > memory on the system. You're asking grompp to decouple
>> a huge amount of degrees
>> > of freedom, which will require a lot of memory to do.
>> It sounds like it's
>> > working, in any case, so there's no real problem.
>> >
>> > Whether or not simultaneously decoupling the LJ and
>> Coulombic interactions of a
>> > whole protein will generate a stable trajectory or
>> sensible result is another
>> > matter.
>> >
>> > -Justin
>> >
>> > > ***********output of grompp*****************
>> > >
>> > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
>> > > Generated 2278 of the 2278 non-bonded parameter
>> combinations
>> > > Generating 1-4 interactions: fudge = 0.5
>> > > Generated 2278 of the 2278 1-4 parameter combinations
>> > > Excluding 3 bonded neighbours molecule type 'Protein'
>> > > turning H bonds into constraints...
>> > > Excluding 2 bonded neighbours molecule type 'SOL'
>> > > turning H bonds into constraints...
>> > > Coupling 1 copies of molecule type 'Protein'
>> > > Setting gen_seed to 8552
>> > > Velocities were taken from a Maxwell distribution at 300 K
>> > > ********************************
>> > >
>> > > Command line and mdp file:
>> > >
>> > > ******************************
>> > > grompp -f pr1.mdp -c after_em.gro -t em.trr -p
>> topol.top -o pr1
>> > > ******************************
>> > > define = -DPOSRES ; position restrain the protein
>> > > ; Run parameters
>> > > integrator = sd ; leap-frog integrator
>> > > nsteps = 5000 ; 2 * 50000 = 100 ps
>> > > dt = 0.002 ; 2 fs
>> > > ; Output control
>> > > nstxout = 1000 ; save coordinates every 2 ps
>> > > nstvout = 5000 ; save velocities every 100ps
>> > > nstenergy = 1000 ; save energies every 2 ps
>> > > nstlog = 1000 ; update log file every 2 ps
>> > > ; Bond parameters
>> > > continuation = no ; first dynamics run
>> > > constraint_algorithm = lincs ; holonomic constraints
>> > > constraints = hbonds ; H bonds constrained
>> > > lincs_iter = 1 ; accuracy of LINCS
>> > > lincs_order = 4 ; also related to accuracy
>> > > ; Neighborsearching
>> > > ns_type = grid ; search neighboring grid cels
>> > > nstlist = 10 ; 20 fs
>> > > rlist = 0.8 ; short-range neighborlist cutoff (in nm)
>> > > rcoulomb = 0.8 ; short-range electrostatic cutoff (in nm)
>> > > rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
>> > > ; Electrostatics
>> > > coulombtype = PME ; Particle Mesh Ewald for long-range
>> electrostatics
>> > > pme_order = 4 ; cubic interpolation
>> > > fourierspacing = 0.12 ; grid spacing for FFT
>> > > ; Temperature coupling is on
>> > > tcoupl = V-rescale ; modified Berendsen thermostat
>> > > tc-grps = Protein Non-Protein ; two coupling groups -
>> more accurate
>> > > tau_t = 0.1 0.1 ; time constant, in ps
>> > > ref_t = 300 300 ; reference temperature, one for each
>> group, in K
>> > > ; Pressure coupling is off
>> > > pcoupl = no ; no pressure coupling in NVT
>> > > ; Periodic boundary conditions
>> > > pbc = xyz ; 3-D PBC
>> > > ; Dispersion correction
>> > > DispCorr = EnerPres ; account for cut-off vdW scheme
>> > > ; Velocity generation
>> > > gen_vel = yes ; assign velocities from Maxwell
>> distribution
>> > > gen_temp = 300 ; temperature for Maxwell distribution
>> > > gen_seed = -1 ; generate a random seed
>> > > ;free energy stuff
>> > > free_energy = yes
>> > > init_lambda = 0.0
>> > > delta_lambda = 0
>> > > sc_alpha =0.5
>> > > sc-power =1.0
>> > > sc-sigma = 0.3
>> > > couple-moltype = Protein
>> > > couple-lambda0 = vdw-q
>> > > couple-lambda1 = none
>> > > *******************************
>> > >
>> > > thanks.
>> > >
>> > > dawei
>> > >
>> > >
>> > >
>> > >
>> > > On Mon, Feb 7, 2011 at 1:05 PM, TJ Mustard
>> <mustardt at onid.orst.edu <mailto:mustardt at onid.orst.edu>
>> > > <mailto:mustardt at onid.orst.edu
>> <mailto:mustardt at onid.orst.edu>>> wrote:
>> > >
>> > > Dawei,
>> > >
>> > >
>> > >
>> > > I have no problems with proteins in the thousands
>> of atoms. Can you
>> > > post your command line and mdp files?
>> > >
>> > >
>> > >
>> > > Thank you,
>> > >
>> > > TJ Mustard
>> > >
>> > >
>> > > On February 7, 2011 at 9:31 AM Da-Wei Li
>> <lidawei at gmail.com <mailto:lidawei at gmail.com>
>> > > <mailto:lidawei at gmail.com
>> <mailto:lidawei at gmail.com>>> wrote:
>> > >
>> > >> Well. It actually isn't dead but becomes very
>> slow for large
>> > >> proteins. dawei
>> > >>
>> > >> On Mon, Feb 7, 2011 at 11:44 AM, Da-Wei Li
>> <lidawei at gmail.com <mailto:lidawei at gmail.com>
>> > >> <mailto:lidawei at gmail.com
>> <mailto:lidawei at gmail.com>>> wrote:
>> > >>
>> > >> hi,
>> > >> I did more test and found that it depended on
>> size of the
>> > >> protein. Grompp will die when number of atoms
>> of the protein
>> > >> is larger than about 200. Is it possible the
>> source code limit
>> > >> the size of the protein that can be decoupled?
>> > >> thanks.
>> > >> dawei
>> > >>
>> > >>
>> > >> On Mon, Feb 7, 2011 at 10:34 AM, Da-Wei Li
>> <lidawei at gmail.com <mailto:lidawei at gmail.com>
>> > >> <mailto:lidawei at gmail.com
>> <mailto:lidawei at gmail.com>>> wrote:
>> > >>
>> > >> Dear users
>> > >> I tried free energy calculation but
>> grompp couldn't go
>> > >> through. It stops after
>> > >> *******************
>> > >> Generated 2278 of the 2278 non-bonded
>> parameter combinations
>> > >> Generating 1-4 interactions: fudge = 0.5
>> > >> Generated 2278 of the 2278 1-4 parameter
>> combinations
>> > >> Excluding 3 bonded neighbours molecule
>> type 'Protein'
>> > >> turning H bonds into constraints...
>> > >> Excluding 2 bonded neighbours molecule
>> type 'SOL'
>> > >> turning H bonds into constraints...
>> > >> Excluding 1 bonded neighbours molecule
>> type 'CL'
>> > >> turning H bonds into constraints...
>> > >> Coupling 1 copies of molecule type 'Protein'
>> > >> *******************
>> > >> The CPU usage is 100%.
>> > >> I just add following into the mdp file:
>> > >> ***************
>> > >> free_energy = yes
>> > >> init_lambda = 0.0
>> > >> delta_lambda = 0
>> > >> sc_alpha =0.5
>> > >> sc-power =1.0
>> > >> sc-sigma = 0.3
>> > >> couple-moltype = Protein
>> > >> couple-lambda0 = vdw-q
>> > >> couple-lambda1 = none
>> > >> ***************
>> > >> Does anyone have some idea about this
>> problem? thanks.
>> > >> Another question is whether I can switch
>> off "two
>> > >> molecules" (such as protein+ligand) in
>> free energy
>> > >> calculation? I searched this list and got
>> that 4.0.7 did
>> > >> support this. how about 4.5.4?
>> > >> dawei
>> > >>
>> > >>
>> > >
>> > >
>> > > TJ Mustard
>> > > Email: mustardt at onid.orst.edu
>> <mailto:mustardt at onid.orst.edu>
>> <mailto:mustardt at onid.orst.edu
>> <mailto:mustardt at onid.orst.edu>>
>> > >
>> > >
>> > > --
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>> >
>> > --
>> > ========================================
>> >
>> > Justin A. Lemkul
>> > Ph.D. Candidate
>> > ICTAS Doctoral Scholar
>> > MILES-IGERT Trainee
>> > Department of Biochemistry
>> > Virginia Tech
>> > Blacksburg, VA
>> > jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >
>> > ========================================
>> > --
>> > gmx-users mailing list gmx-users at gromacs.org
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>>
>>
>>
>> TJ Mustard
>> Email: mustardt at onid.orst.edu <mailto:mustardt at onid.orst.edu>
>>
>>
>> --
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>
>
>
> TJ Mustard
> Email: mustardt at onid.orst.edu <mailto:mustardt at onid.orst.edu>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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