[gmx-users] Re: free energy calculation , grompp crash

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 8 00:58:12 CET 2011



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 <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
>          >
>          > ========================================
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> 
>          
> 
>         TJ Mustard
>         Email: 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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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