[gmx-users] Re: gmx-users Digest, Vol 58, Issue 59
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 11 14:08:44 CET 2009
Robert Fenwick wrote:
>
> pdb2gmx -f prot1LYD.pdb -ter -ignh -vsite hydrogens -water tip3p
> select OPLS, 0, 0
The benchmarks were done with SPC/E; don't know if that will make a difference
or not (probably not, but just FYI).
>
> editconf -f conf.gro -bt dodecahedron -d 0.7 -o box.gro
>
This box will be smaller than what was described in the paper. Try -box 7 7 7
for a more reasonable size (and total number of water molecules).
> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
>
> grompp -f em.mdp -p topol.top -c solvated.gro -o sol.tpr
>
> genion -s sol.tpr -nn 8 -nname CL- -nq -1 -np 0 -pname NA+ -pq 1 -p
> topol.top -o solvatedIon.gro
> select 12 (SOL)
>
> grompp -f em.mdp -p topol.top -c solvatedIon.gro -o em.tpr
>
> mdrun -v -deffnm em
>
> grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr
>
> mpirun -np 16 mdrun_mpi -v -deffnm pr -npme 8
>
You're bound to get bad performance doing this. You've got a 1:1 PP:PME ratio.
If you've done everything correctly, grompp should estimate that the PME load
be about 33%, thus 2:1 PP:PME. I ran this particular benchmark on our cluster
using 12 nodes, with 4 for PME.
> grompp -f run.mdp -p topol.top -c pr.gro -o run.tpr
>
> mpirun -np 16 mdrun_mpi -v -deffnm run -npme 8
>
> The inputs are, and come directly from the article Hess et al., 2008
> JCTC GROMACS 4 :
>
> ::::::::::::::
> em.mdp
> ::::::::::::::
> integrator = steep
> nsteps = 200
> nstlist = 10
> rlist = 1.0
> coulombtype = pme
> fourierspacing = 0.125
> rcoulomb = 1.0
> vdw-type = cut-off
> rvdw = 1.0
> lincs-order = 6
> nstenergy = 10
> ::::::::::::::
> pr.mdp
> ::::::::::::::
> integrator = md
> nsteps = 50000
> dt = 0.002
> nstlist = 10
> rlist = 1.0
> coulombtype = pme
> fourierspacing = 0.125
> rcoulomb = 1.0
> vdw-type = cut-off
> rvdw = 1.0
> lincs-order = 6
> tcoupl = Berendsen
> tc-grps = protein non-protein
> tau-t = 0.1 0.1
> ref-t = 298 298
> Pcoupl = Berendsen
> tau-p = 1.0
> compressibility = 1e-5 1e-5 1e-5 0 0 0
> ref-p = 1.0
> nstenergy = 100
> define = -DPOSRES
>
> ::::::::::::::
> run.mdp
> ::::::::::::::
> integrator = md
> nsteps = 50000
> dt = 0.004
> nstlist = 5
> rlist = 1.0
> coulombtype = pme
> fourierspacing = 0.125
> rcoulomb = 1.0
> vdw-type = cut-off
> rvdw = 1.0
> lincs-order = 6
> tcoupl = Berendsen
> tc-grps = protein non-protein
> tau-t = 0.1 0.1
> ref-t = 298 298
> nstxout = 1000
> nstvout = 1000
> nstxtcout = 100
> nstenergy = 100
>
Try applying "constraints = all-bonds" (based on Table 3 of Berk's JCTC paper
about P-LINCS).
-Justin
> The simulation dies with:
>
> Step 6, time 0.024 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.222533, max 1.229818 (between atoms 328 and 329)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 1970 1973 90.0 0.2413 0.3543 0.1930
> 1888 1891 65.8 0.4413 0.1879 0.1930
> 447 449 59.2 0.2406 0.1939 0.1939
> 656 660 90.0 0.1930 0.4267 0.1930
> 616 619 90.0 0.1924 0.2612 0.1930
> 477 480 89.9 0.2945 0.3802 0.1930
> 319 329 65.3 0.1670 0.1816 0.1670
> 328 329 90.0 0.0915 0.2039 0.0915
> 762 765 42.4 0.1584 0.1554 0.1583
> 762 766 44.0 0.1581 0.1616 0.1583
>
> t = 0.024 ps: Water molecule starting at atom 16419 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates
> Warning: 1-4 interaction between 949 and 963 at distance 6.212 which
> is larger than the 1-4 table size 2.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Warning: 1-4 interaction between 747 and 753 at distance 14.118 which
> is larger than the 1-4 table size 2.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.3
> Source code file: pme.c, line: 518
>
> Fatal error:
> 11 particles communicated to PME node 3 are more than a cell length
> out of the domain decomposition cell of their charge group
> -------------------------------------------------------
>
>
>> The methodology for the lysozyme benchmark is pretty explicit in the Gromacs 4
>> paper; is there some aspect that is not clear?
>
> I agree that the paper is clear, I ask because it is obvious that I am
> doing something wrong the system should be stable!
>
>> -Justin
>>
>>> Bryn
>>> _______________________________________________
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>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> 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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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