[gmx-users] Re: gmx-users Digest, Vol 58, Issue 59
Robert Fenwick
robert.fenwick at irbbarcelona.org
Wed Feb 11 13:49:31 CET 2009
> Robert Fenwick wrote:
>> Hi,
>>
>> I wanted to run one of the gromacs 4.0 benchmarks on a new cluster
>> that we have and also wanted to see the affect of this 4 fs time step.
>> If it would not be too much trouble would it be possible for the
>> setups of either the PLINCS paper or the GROMACS 4.0 paper to be
>> placed somewhere on the website. Specifically I am intersted in the
>> lysozyme benchmark, however I suspect others might like the membrane
>> system to as well.
>>
>> I have tried to set a similar simulation up, but it is not able to run
>> with 4 fs integration.
>>
>
> So what exactly is going wrong? What is in your .mdp file? It is probably
> better for you to post this information here and receive feedback, so that
> others can make use of it later.
I've followed what I think is a sensible setup, which comes from the
GROMACS workshop pre-workshop tutorial. Comments are wellcome, I
generate this using a bash script for convenience:
grep -v HOH original/1LYD.pdb > ./prot1LYD.pdb
pdb2gmx -f prot1LYD.pdb -ter -ignh -vsite hydrogens -water tip3p
select OPLS, 0, 0
editconf -f conf.gro -bt dodecahedron -d 0.7 -o box.gro
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
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
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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