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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