Dear all,<div><br></div><div>Zephyr (<a href="https://simtk.org/home/zephyr">https://simtk.org/home/zephyr</a>) is released, although only for Mac and Windows so far, and it comes with examples, pretty neat.</div><div><br>
</div><div>Even though there's some apparently fixes compared to the usual release of openmm and gromacs-openmm, my molecule didn't work with it yet.</div><div><br></div><div>Nevertheless, for those with nvidia cuda and Mac or Windows, it's worth trying.</div>
<div><br></div><div>Cheers,</div><div>Alan<br><br><div class="gmail_quote">On Sat, Jul 18, 2009 at 18:31, Alan <span dir="ltr"><<a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Thanks Justin.<br>
<br>
I could swear I tried what you said... anyway it worked now (2.5 x<br>
faster), but not with implicit solvent for mdrun-openmm... Trying with<br>
plain mdrun with the setup for implicit solvent and it seemed to work<br>
(although I don't know how to interpret this from<br>
GromacsOpenMMPreview3-Mac/Gromacs-OpenMM Readme.txt file: "even though<br>
this is not available in the standard Gromacs 4")<br>
<br>
I still would like an example/tutorial that really worked for someone<br>
with gmx openmm.<br>
<br>
In the end, with mdrun-openmm and implicit solvent in the mdp file, I<br>
got a file md.gro full of "nan nan".<br>
<br>
For those interested, here are the commands I did. If you have GMX<br>
with ffamber, CUDA and GMX-openmm you may reproduce it.<br>
<br>
###############################<br>
<br>
cat << EOF >| em.mdp<br>
define = -DFLEXIBLE<br>
integrator = cg ; steep<br>
nsteps = 200<br>
constraints = none<br>
emtol = 1000.0<br>
nstcgsteep = 10 ; do a steep every 10 steps of cg<br>
emstep = 0.01 ; used with steep<br>
nstcomm = 1<br>
coulombtype = Reaction-Field<br>
ns_type = simple<br>
rlist = 1.2<br>
<div class="im">rcoulomb = 1.2<br>
rvdw = 1.2<br>
vdwtype = cut-off<br>
</div>Tcoupl = no<br>
Pcoupl = no<br>
gen_vel = no<br>
nstxout = 0 ; write coords every # step<br>
epsilon_rf = 0<br>
pbc = no<br>
EOF<br>
<br>
cat << EOF >| md.mdp<br>
<div class="im">integrator = md<br>
nsteps = 1000<br>
dt = 0.002<br>
constraints = all-bonds<br>
nstcomm = 1<br>
ns_type = simple<br>
</div>rlist = 1.2<br>
<div class="im">rcoulomb = 1.2<br>
rvdw = 1.2<br>
vdwtype = cut-off<br>
coulombtype = Reaction-Field<br>
epsilon_rf = 0<br>
Tcoupl = no<br>
Pcoupl = no<br>
gen_vel = yes<br>
nstxout = 2 ; write coords every # step<br>
lincs-iter = 2<br>
pbc = no<br>
</div>comm_mode = ANGULAR<br>
; uncomment below to test with implicit solvent<br>
;implicit_solvent = GBSA<br>
<div class="im">;gb_algorithm = OBC<br>
;gb_epsilon_solvent = 78.3<br>
</div>EOF<br>
<br>
wget -c "<a href="http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1BVG" target="_blank">http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1BVG</a>"<br>
-O 1BVG.pdb<br>
grep 'ATOM ' 1BVG.pdb>| Protein.pdb<br>
grep 'HETATM' 1BVG.pdb>| Ligand.pdb<br>
<br>
sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g Protein.pdb | sed s/PRO\ B\ \ \<br>
1/NPROB\ \ \ 1/g \<br>
| sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\ \ 99/CPHEB\ \ 99/g \<br>
| sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\ CPHE/OC2\ CPHE/g \<br>
| sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed s/CYS\ /CYN\ /g >|<br>
ProteinAmber.pdb<br>
<br>
# Process with pdb2gmx and define water<br>
pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -ignh<br>
<br>
grompp -f em.mdp -c Protein2.pdb -p Protein.top -o em.tpr<br>
mdrun -v -deffnm em<br>
<br>
grompp -f md.mdp -c em.gro -p Protein.top -o md.tpr<br>
mdrun -v -deffnm md<br>
<br>
vmd md.gro md.trr # OK<br>
<br>
mdrun-openmm -v -deffnm md<br>
# 3 times fater<br>
# works fine without set for implicit solvent in md.mdp<br>
# with implicit solvent, md.gro full of nan nan nan everywhere.<br>
<br>
###############################<br>
<div><div></div><div class="h5"><br>
On Sat, Jul 18, 2009 at 17:31, Alan<<a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a>> wrote:<br>
> Ok, I tried.<br>
><br>
> Can someone tell how to have in a mdp file this combination (in order<br>
> to satisfy gromacs openmm) without raising a error in grompp?<br>
><br>
> ns_type = simple<br>
> pbc = no<br>
> coulombtype = Reaction-Field<br>
><br>
> Whatever I try I get:<br>
><br>
> ERROR: Twin-range neighbour searching (NS) with simple NS algorithm<br>
> not implemented<br>
><br>
> My full md.mdp file is:<br>
> integrator = md<br>
> nsteps = 1000<br>
> dt = 0.002<br>
> constraints = all-bonds<br>
> nstcomm = 1<br>
> ns_type = simple<br>
> rlist = 1.0<br>
> rcoulomb = 1.2<br>
> rvdw = 1.2<br>
> vdwtype = cut-off<br>
> coulombtype = Reaction-Field<br>
> epsilon_rf = 0<br>
> Tcoupl = no<br>
> Pcoupl = no<br>
> gen_vel = yes<br>
> nstxout = 2 ; write coords every # step<br>
> lincs-iter = 2<br>
> pbc = no<br>
> implicit_solvent = GBSA<br>
> gb_algorithm = OBC<br>
> gb_epsilon_solvent = 78.3<br>
> comm_mode = ANGULAR<br>
><br>
><br>
> Many thanks in advance,<br>
><br>
> Alan<br>
><br>
><br>
><br>
> On Sat, Jul 18, 2009 at 11:35, Alan<<a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a>> wrote:<br>
>> Dear Mark,<br>
>><br>
>> Thanks. I reread those file carefully and noticed the "only implicit<br>
>> solvent". Sorry for that. I am building my test case here to see by<br>
>> myself how fast it can be.<br>
>><br>
>> Alan<br>
>><br>
>><br>
>> On Sat, Jul 18, 2009 at 11:00, <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:<br>
>><br>
>>> Alan wrote:<br>
>>>> Hi list, does anyone have an example (input pdb, gmx commands and<br>
>>>> md.mdp for example) to test gromacs with and without openmm?<br>
>>>><br>
>>>> The case I use here (with explicit water) didn't show me any speed up<br>
>>>> (comparing with mpirun -c 2 mdrun_mpi...).<br>
>>>><br>
>>>> I am using Mac Leopard 10.5.7 with Cuda drivers and gromacs 4.0.5<br>
>>><br>
>>> This would be expected if you read the OpenMM README.... or see<br>
>>> <a href="http://oldwiki.gromacs.org/index.php/OpenMM_GROMACS" target="_blank">http://oldwiki.gromacs.org/index.php/OpenMM_GROMACS</a><br>
>>><br>
>>> Mark<br>
>> --<br>
>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
>> Department of Biochemistry, University of Cambridge.<br>
>> 80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>>>><a href="http://www.bio.cam.ac.uk/~awd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
>><br>
><br>
><br>
><br>
> --<br>
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
> Department of Biochemistry, University of Cambridge.<br>
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>>><a href="http://www.bio.cam.ac.uk/~awd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
><br>
<br>
<br>
<br>
</div></div>--<br>
<div><div></div><div class="h5">Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
Department of Biochemistry, University of Cambridge.<br>
80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/~awd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge.<br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div>