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 <lida...@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 <musta...@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" <jalem...@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 <musta...@onid.orst.edu
>> > > <mailto:musta...@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 <lida...@gmail.com
>> > > <mailto:lida...@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 <lida...@gmail.com
>> > >> <mailto:lida...@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 <
>> lida...@gmail.com
>> > >> <mailto:lida...@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: musta...@onid.orst.edu <mailto:musta...@onid.orst.edu>
>> > >
>> > >
>> > > --
>> > > gmx-users mailing list gmx-users@gromacs.org
>> > > <mailto:gmx-users@gromacs.org>
>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > > Please search the archive at
>> > > http://www.gromacs.org/Support/Mailing_Lists/Search before
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>> > > <mailto:gmx-users-requ...@gromacs.org>.
>> > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > >
>> > >
>> >
>> > --
>> > ========================================
>> >
>> > 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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>> >
>>
>>
>>
>> TJ Mustard
>> Email: musta...@onid.orst.edu
>>
>> --
>> gmx-users mailing list gmx-users@gromacs.org
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>
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