[gmx-users] Re: free energy calculation , grompp crash
Justin A. Lemkul
jalemkul at vt.edu
Mon Feb 7 19:23:19 CET 2011
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>> 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>> 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>> 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>> 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>
>
>
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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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