Da-Wei Li 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
It looks like your topology has some serious problems. Bonded interactions
should not occur at 4-nm distance, unless you're using some special distance
restraints, in which case you probably can't make DD work very efficiently;
mdrun -pd might be an option in that case. If you're running a basic protein
simulation without special restraints, etc then something is wrong in the topology.
so that domain decomposition will not work. What is a LJC pair? I did
Some sort of 1-4 interaction, it looks like, but I didn't spend much time in the
code to be absolutely sure.
-Justin
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
<mailto: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
<mailto: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 <mailto: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>
> > <mailto: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>
> > <mailto: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>
> >> <mailto: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>
> >> <mailto: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> <mailto:musta...@onid.orst.edu
<mailto:musta...@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
>
> ========================================
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TJ Mustard
Email: musta...@onid.orst.edu <mailto:musta...@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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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