[gmx-users] MD with DNA double strand

[Amali Guruge]

Dear Gromacs users,

I want to do a molecular dynamic simulation for my enzyme-ligand complex.
The enzyme is topoisomerase I. I used the pdb id 1K4T for the simulation
and I need to keep the DNA double strand with the enzyme.

I replaced the 5'-sulfhydryl group into a 5'-hydroxyl group before starting
the simulation.

I gave the command 'pdb2gmx -f receptor.pdb -inter -p system.top -o
recep01.pdb -ignh'. I selected AMBER99 as the force field while SPC/E was
used as the water model.
Then I got the following error.

Fatal error:
Atom O in residue DG 11 was not found in rtp entry DG with 33 atoms
while sorting atoms.

How can I solve this problem? Can anyone help me?

Thank you.
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Re: [gmx-users] Fw:Re: on CHARMM-GUI produced lipid bilayer for gromacs use

[Tsjerk Wassenaar]

Brett,

Please do not mail me directly with such questions. I am not your tutor and
I am not involved in the CHARMM-GUI. I forward this mail to the gromacs
user list, as there may be someone who can and is willing to give
suggestions there. But I do also like to note that the CHARMM-GUI is not
Gromacs and that it may be better to contact the authors there or to see if
they have a user forum.

Cheers,

Tsjerk

On Thu, Sep 17, 2015 at 9:51 AM, Brett  wrote:

> Dear Tsjerk,
>
> Thanks for your reply. When using CHARM-GUI lipid bilayer builder, I have
> met the following problems, which I hope you can answer.
>
> For step 1, there is "Generate Pore Water and Measure Pore Size". What is
> the function of "Generate Pore Water and Measure Pore Size"? Should I click
> it or not?
>
> For step 2, thers is "determines system size based on lipid layers between
> neighboring proteins (default 1.5)". Where there are lipid bilayers between
> neighboring proteins? I think the lipid bilayer should only exist in the
> trans-membrane part of the membrane protein.
>
> For step 3, there is "Check lipid ring (and protein surface) penetration
> "? What is this for? Should I click it or not?
>
> For step 5, there is "NPT ensemble ", “NPAT ensemble”and “NPgT ensemble”.
> I regard the "NPT" has the same meaning as the "MPT" used in gromacs
> on-line tutorial, then what is “NPAT ensemble”and “NPgT ensemble”?
>
> For step 6, in step 5 I have selected "NPT ensemble" and I only select
> gromacs output. Attached image was the snapshort of the results from step
> 6. It seems it did not contain the the .top file as you mentoned in youe
> e-mail. Did I do something wrong?
>
> Next step, if for the PDB as mentioned in the attached snapshort image, I
> delete all the H2O, and then I start it with the H2O deleted PDB fom the
> pdb2gmx step, in the step to add water box, it is rather clear water will
> be added and in the surronding edge of the lipid, how the gromacs process
> the contact between water and the lipid tail of the lipid bilayer?
>
> I am looking forward to getting a reply from you.
>
> Best regards.
>
> Brett
>
>
>
>
>
>
>
>  Forwarding messages 
> From: "Tsjerk Wassenaar" 
> Date: 2015-09-17 13:57:37
> To:  "Discussion list for GROMACS users" 
> Subject: Re: [gmx-users] on CHARMM-GUI produced lipid bilayer for gromacs use
> Hi Brett,
>
> The CHARMM-GUI also provides the .top file. You can use that and the PDB
> (it doesn't need to be .gro) to run grompp.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Sep 17, 2015 at 5:06 AM, Brett  wrote:
>
> > Dear All,
> >
> >
> > After I got the membrane protein PDB with the membrane part packed in
> > lipid bilayer by the lipid bilayer builder of CHARMM-GUI, will you please
> > let me know how to get the inputs for the gromacs next step MD process？ For
> > example， if I wand to go directly to the nvt equilibration step with the
> > CHARMM-GUI produced PDB, the command in the lysozyme tutorial is "gmx
> > grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr". Then will you please
> > let me know how to get the input *.gro and *.top file in order to get the
> > *.tpr file? Or for the  CHARMM-GUI produced PDB, I delete all the H2O, and
> > then start from the pdb2gmx step with the PDB file containing only the
> > membrane protein and the lipid bilayer? But in this way it seems the sides
> > of the lipid bilayer will also be packed in H2O.
> >
> >
> > I am looking forward to getting a reply from you.
> >
> >
> > Best regards.
> >
> >
> > Brett
> >
> >
> >
> >
> >
> >
> > --
> > Gromacs Users mailing list
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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>
>
>



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Re: [gmx-users] Choose index group from terminal input.

[Mark Abraham]

Hi,

Yes. Further options at
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

Mark

On Thu, Sep 17, 2015 at 1:04 PM Dawid das  wrote:

> O'right, I have figured that out myself. Just use text file like data.txt
> with two lines:
> 1
> 1
>
> and redirect it: g_rms [options] < data.txt
>
> 2015-09-17 11:32 GMT+01:00 Dawid das :
>
> > Dear Gromacs Experts,
> >
> > Let's say that for some reasons I don't want to specify the atom group
> > when g_rms (or other module) prompts me to do so.
> > So I do not want to see this:
> >
> > Select group for RMSD calculation
> > Group 0 ( System) has 38387 elements
> > Group 1 (Protein) has  3470 elements
> > Group 2 (  Protein-H) has  1772 elements
> > Group 3 (C-alpha) has   217 elements
> > Group 4 (   Backbone) has   653 elements
> > Group 5 (  MainChain) has   869 elements
> > Group 6 (   MainChain+Cb) has  1065 elements
> > Group 7 (MainChain+H) has  1076 elements
> > Group 8 (  SideChain) has  2394 elements
> > Group 9 (SideChain-H) has   903 elements
> > Group10 (Prot-Masses) has  3461 elements
> > Group11 (non-Protein) has 34917 elements
> > Group12 (  Water) has 34845 elements
> > Group13 (SOL) has 34845 elements
> > Group14 (  non-Water) has  3542 elements
> > Group15 (Ion) has72 elements
> > Group16 ( NA) has37 elements
> > Group17 ( CL) has35 elements
> > Group18 ( Water_and_ions) has 34917 elements
> > Group19 (Chromophore) has37 elements
> > Select a group: 1
> > Selected 1: 'Protein'
> >
> > and I want to specify this Group 1 (Protein) in my command, e.g.
> > g_rms -s ../npt-md2.tpr -f ../npt-md2.xtc -tu ns -b 0 -e 100 -n
> > ../index.ndx -o rmsd-0-100.xvg
> > -some_option 1
> > Is it possible?
> >
> >
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Re: [gmx-users] Electric double layer, how to add charge

[Andreas]

Hello,

thanks, very simple, changing the .top file worked perfectly.
And I was thinking: How do I change the .gro file, will changing the
.top be enough.

thanks for the advice with the potential. I was thinking to calculate
the potential (voltage) with the the poissons equation and the ion
density. Afterwards to use the charge on my graphene layer to calculate
the double layer capacitance (C_dl) and then maybe to show a C_dl change
over voltage.
(by changing the charge, starting with a very small one. At a certain
"voltage"(actually charge) the Cdl should stay about constant, i guess).

Data will be used to estimate a more complex structure, sadly there is
no direct comparison possible.

Do you know if there are better alternatives to the OPLSAA, in Gromacs,
for graphene edls? How to solve the problem with the potential?

Thanks again.

Best regards

Andreas

On Wed, Sep 16, 2015 at 23:33, André Farias de Moura wrote:


you should edit your topology file (either top or itp) to include explicit
charges to each atom.

regarding the proper choice of charges, it depends on the surface potential
you think your system should have (mind that OPLSAA will typically produce
an overestimated potential as compared to experiment, if available - from
my experience it may be 2-3 times larger)

adding charges with opposite signs in different layers work as well, you
just need to keep track of the layer in which each atom is located and then
edit the topology files accordingly (in this case, you'll have a neutral,
polar interface, as compared to the electrically charged interface obtained
using only charges of the same sign)

best

André

On Wed, Sep 16, 2015 at 5:45 PM, Andreas  wrote:


Hello users,

I want to simulate a graphene electric double layer (edl). So far i have
used the cnt tutorials and the tutorial for lysozyme in water.
All modification to the OPLSAA field parameter (atomname2type.n2t,
atomtypes.atp, ffbonded.itp, ffnonbonded.itp) which i have done were with
zero charge and i could already simulate a graphite layer in a box filled
with water and ions, similar to the lysozyme tutorial.

How and then to add a charge to the graphene layer, or if two graphene
layers are added, how to add opposite charges to them?

Or is there a more simple way to MD simulate an edl, in gromacs,
altogether?

I would be very thankful for any help

Best regards

Andreas
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[gmx-users] Choose index group from terminal input.

[Dawid das]

Dear Gromacs Experts,

Let's say that for some reasons I don't want to specify the atom group when
g_rms (or other module) prompts me to do so.
So I do not want to see this:

Select group for RMSD calculation
Group 0 ( System) has 38387 elements
Group 1 (Protein) has  3470 elements
Group 2 (  Protein-H) has  1772 elements
Group 3 (C-alpha) has   217 elements
Group 4 (   Backbone) has   653 elements
Group 5 (  MainChain) has   869 elements
Group 6 (   MainChain+Cb) has  1065 elements
Group 7 (MainChain+H) has  1076 elements
Group 8 (  SideChain) has  2394 elements
Group 9 (SideChain-H) has   903 elements
Group10 (Prot-Masses) has  3461 elements
Group11 (non-Protein) has 34917 elements
Group12 (  Water) has 34845 elements
Group13 (SOL) has 34845 elements
Group14 (  non-Water) has  3542 elements
Group15 (Ion) has72 elements
Group16 ( NA) has37 elements
Group17 ( CL) has35 elements
Group18 ( Water_and_ions) has 34917 elements
Group19 (Chromophore) has37 elements
Select a group: 1
Selected 1: 'Protein'

and I want to specify this Group 1 (Protein) in my command, e.g.
g_rms -s ../npt-md2.tpr -f ../npt-md2.xtc -tu ns -b 0 -e 100 -n
../index.ndx -o rmsd-0-100.xvg
-some_option 1
Is it possible?
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Re: [gmx-users] Choose index group from terminal input.

[Dawid das]

O'right, I have figured that out myself. Just use text file like data.txt
with two lines:
1
1

and redirect it: g_rms [options] < data.txt

2015-09-17 11:32 GMT+01:00 Dawid das :

> Dear Gromacs Experts,
>
> Let's say that for some reasons I don't want to specify the atom group
> when g_rms (or other module) prompts me to do so.
> So I do not want to see this:
>
> Select group for RMSD calculation
> Group 0 ( System) has 38387 elements
> Group 1 (Protein) has  3470 elements
> Group 2 (  Protein-H) has  1772 elements
> Group 3 (C-alpha) has   217 elements
> Group 4 (   Backbone) has   653 elements
> Group 5 (  MainChain) has   869 elements
> Group 6 (   MainChain+Cb) has  1065 elements
> Group 7 (MainChain+H) has  1076 elements
> Group 8 (  SideChain) has  2394 elements
> Group 9 (SideChain-H) has   903 elements
> Group10 (Prot-Masses) has  3461 elements
> Group11 (non-Protein) has 34917 elements
> Group12 (  Water) has 34845 elements
> Group13 (SOL) has 34845 elements
> Group14 (  non-Water) has  3542 elements
> Group15 (Ion) has72 elements
> Group16 ( NA) has37 elements
> Group17 ( CL) has35 elements
> Group18 ( Water_and_ions) has 34917 elements
> Group19 (Chromophore) has37 elements
> Select a group: 1
> Selected 1: 'Protein'
>
> and I want to specify this Group 1 (Protein) in my command, e.g.
> g_rms -s ../npt-md2.tpr -f ../npt-md2.xtc -tu ns -b 0 -e 100 -n
> ../index.ndx -o rmsd-0-100.xvg
> -some_option 1
> Is it possible?
>
>
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[gmx-users] Problem with wall!

[mahi heyran]

Dear all,

I am a new gromacs user. I want to simulate a box with two charged walls
contain water molecules, but i face to many problems! for example water
molecules go out of box.
Could anyone help me by explain details of wall simulation?

Thanks in advance.

Mahi
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Re: [gmx-users] GPU-accelerated desktop PC for MD simulations

[Szilárd Páll]

Hi,

The workstation hardware benchmarked in our recent paper [1] is quite
decent. You should also browse the past discussions on the list.

For best performance in a desktop setup a Haswell-E CPU (i7 4960X or 4930)
and a GTX 980/980 Ti is the best bet, for something mid-range I'd go with a
high-clocked Core i5 CPU and a GTX 970 or 960.


[1] http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030

--
Szilárd

On Thu, Sep 17, 2015 at 3:18 AM, Gustavo Avelar Molina <
avelarmolinagust...@gmail.com> wrote:

> Hi everyone,
>
> I want to build a new GPU-accelerated desktop PC for MD simulations of
> relatively simple protein/carbohydrate systems. No QM-MM simulations is
> intended for now. For instance, I have been working with a protein of
> approximately 1500 atoms in the presence of small carbohydrates (<100
> atoms). For the protein alone, my home PC (i5-4570 CPU 3.20GHz, not
> GPU-accelerated) does approximately 5 ns/day, so I want something
> considerably faster than that.
>
> Which hardware should I choose? Could you suggest low to high price
> configurations with good power considering the current technology
> available?
>
> Thank you very much for your time.
>
> Best regards,
>
> Gustavo
>
> ==
> Gustavo Avelar Molina, B.Sc. Chem.
> M.Sc. Chem. Student
>
> Department of Chemistry
> Faculty of Philosophy, Sciences and Literature of Ribeirão Preto
> Protein Biochemistry and Biophysics Laboratory
> University of São Paulo, Ribeirão Preto, São Paulo, Brazil
>
> +55 16 994311221 | +55 11 949874141
>
> avelarmolinagust...@gmail.com | gustavoavelarmol...@usp.br
>
> https://lbbpusp.wordpress.com/ |
>
> 
> <
> https://www.dropbox.com/s/knqpqnehdpj4qfr/Gustavo%20Avelar%20Molina%20CV.pdf?dl=0
> >
> 
>
> ==
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Re: [gmx-users] GPU-accelerated desktop PC for MD simulations

[Justin Lemkul]

On 9/16/15 9:18 PM, Gustavo Avelar Molina wrote:

Hi everyone,

I want to build a new GPU-accelerated desktop PC for MD simulations of
relatively simple protein/carbohydrate systems. No QM-MM simulations is
intended for now. For instance, I have been working with a protein of
approximately 1500 atoms in the presence of small carbohydrates (<100
atoms). For the protein alone, my home PC (i5-4570 CPU 3.20GHz, not
GPU-accelerated) does approximately 5 ns/day, so I want something
considerably faster than that.

Which hardware should I choose? Could you suggest low to high price
configurations with good power considering the current technology available?



http://dx.doi.org/10.1002/jcc.24030
http://dx.doi.org/10.1007/978-3-319-15976-8_1
http://pubman.mpdl.mpg.de/pubman/item/escidoc:2037317/component/escidoc:2037318/2037317.pdf?mode=download

This question gets asked a few times a week, it seems, so please do some Google 
searching and refer to the information about GPUs posted on gromacs.org.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Efficiently running multiple simulations

[Zimmerman, Maxwell]

Hi Mark,

Thank you for reviewing the log files! I will recompile GROMACS for AVX2_256 
SIMD to efficiently use the CPUs.

The number of cores on the node is 16 and each core has two threads. By 
default, GROMACS picked 4 threads per simulation. I reran the simulation by 
specifying 2 threads per simulation and am providing a link to the new log 
file. I still see the same results, which is a lower performance per simulation 
when using 8 simulations on the node opposed to just 1.

https://www.dropbox.com/s/rd3akpqcn3mo7c5/md_8GPUs_2Cores.log?dl=0

My problem isn't that I am confusing "node" with "simulation", but rather that 
each of the 8 log files (each log file corresponds to a single simulation of 
the 8 that were run using "-multi") shows mapping to 8 GPUs. Is each log file 
telling me that the simulations are all aware of each other, or is each 
simulation trying to create 8 domains to split up on the GPUs?

I am still puzzled as to the loss in performance with increasing number of 
simulations on the node. I tried running 2 simulations with 2 GPUs and 4 CPUs, 
4 simulations with 4 GPUs and 8 CPUs, and 6 simulations with 6 GPUs and 12 
CPUs. For the increasing number of simulations on the node, I see a greater 
loss in performance for individual simulations.

Regards,
-Maxwell

___
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Wednesday, September 16, 2015 4:44 PM
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Efficiently running multiple simulations

Hi,

The log files tell you that you should compile for AVX2_256 SIMD for the
Haswell CPUs you have. Do that. Your runs are wasting a fair chunk of the
value of the CPU hardware, and your setup absolutely needs to extract every
last drop from the CPUs. That means you need to follow the instructions in
the GROMACS install guide, which suggest you use a recent compiler. Your
GROMACS was compiled with gcc 4.4.7, which was about two years old before a
Haswell was sold! Why HPC clusters buy the latest hardware and continue to
default to the "stable" 5-year old compiler suite shipped with the
"enterprise" distribution remains a total mystery to me. :-)

The log file also says that your MPI system is starting four OpenMP threads
per rank in the multi-simulation case, so the comparison is not valid.
Starting 8*4 OpenMP threads on your node oversubscribes the actual cores,
and this is terrible for GROMACS. You need to find out how many actual
cores you have (each of which can have two hyperthreads, which is usually
worth using on such Haswell machines). You want either one thread per core,
or two threads per core (try both). If you don't know how many actual cores
there are, consult your local docs/admins.

"Mapping of GPUs to the 8 PP ranks in this node: #0, #1, #2, #3, #4, #5,
#6, #7" is actually correct and unambiguous. There's 8 simulations, each
with 1 domain, so 8 PP ranks, and each is mapped to one of 8 GPUs *in this
node*. You've been reading "node" and thinking "simulation."

Mark


On Wed, Sep 16, 2015 at 9:23 PM Zimmerman, Maxwell 
wrote:

> Hi Mark,
>
> Here are two links to .log files for running 1 simulation on 1 GPU and 2
> CPUs and 8 simulations across all 8 GPUs and 16 CPUs respectively:
>
> https://www.dropbox.com/s/ko2l0qlr4kdpt51/md_1GPU.log?dl=0
> https://www.dropbox.com/s/chtcv4nqxof64p8/md_8GPUs.log?dl=0
>
> Regards,
> -Maxwell
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Wednesday, September 16, 2015 1:39 PM
> To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Efficiently running multiple simulations
>
> Hi,
>
> On Wed, Sep 16, 2015 at 5:46 PM Zimmerman, Maxwell 
> wrote:
>
> > Hi Mark,
> >
> > Thank you for the feedback.
> >
> > To ensure that I am making a proper comparison, I tried running:
> > mpirun -np 1 mdrun_mpi -ntomp 2 -gpu_id 0 -pin on
> > and I still see the same pattern; running a single simulation with 1 GPU
> > and 2 CPUs performs nearly twice as well as running 8 simulations with
> > "-multi" using 8 GPUs and 16 CPUs.
> >
>
> OK. In that case, please share some links to .log files on a file-sharing
> service, so we might be able to see where the issue arises. The list does
> not accept attachments.
>
> Just to clarify, when I use "-multi" all 8 of the .log files show that 8
> > GPUs are selected for the run. If a single GPU were being used, wouldn't
> it
> > only show mapping to one GPU ID per .log file?
> >
>
> I forget the details here, but organizing the mapping has to be done on a
> per-node basis. It would not surprise me if the reporting was not strictly

Re: [gmx-users] Atomic charges

[M.Cristina Donnamaria]

Hello, from  my own expierence I can say that
atomic charges calculated with Gaussian are good charges.

2015-09-17 1:37 GMT-03:00 Pallavi Banerjee <
pallavis...@students.iiserpune.ac.in>:

> Thanks Justin. Things are clearer now.
>
> -Pallavi Banerjee
> --
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Re: [gmx-users] MD with DNA double strand

[Justin Lemkul]

On 9/17/15 2:03 AM, Amali Guruge wrote:

Dear Gromacs users,

I want to do a molecular dynamic simulation for my enzyme-ligand complex.
The enzyme is topoisomerase I. I used the pdb id 1K4T for the simulation
and I need to keep the DNA double strand with the enzyme.

I replaced the 5'-sulfhydryl group into a 5'-hydroxyl group before starting
the simulation.

I gave the command 'pdb2gmx -f receptor.pdb -inter -p system.top -o
recep01.pdb -ignh'. I selected AMBER99 as the force field while SPC/E was
used as the water model.
Then I got the following error.

Fatal error:
Atom O in residue DG 11 was not found in rtp entry DG with 33 atoms
while sorting atoms.

How can I solve this problem? Can anyone help me?



You need to make sure the protein and each DNA strand are in separate chains, 
then interactively select appropriate termini with pdb2gmx -ter.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] energygrps interactions are 0 for water

[Julian Michalowsky]

Hi,

I have a problem regarding the calculation of interaction energies using
gmx energy and the energygrps parameter in the mdp file. My mdp file
includes the line

energygrps = Ion OW

Whenever I calculate the LJ-SR and Coul.-SR energy terms between OW
and any other energy group, the result is just zero. I am using an
appropriate
index file during preprocessing that defines OW as a group and also tried
SOL and Water as energygrps in the mdp file.

I originally used this with a custom force field, but encountered the same
problem during a test run using the gromos54a7.ff from the default top
directory.

The system is a simple electrolyte solution (NaCl in water). I use a python
script to set up the initial gro file. Ions are referred to as NA, CL in
both gro
and top file (not NA+ or CL-, if that makes any difference). The top file
includes the respective forcefield.itp, ions.itp and spce.itp topologies via
the #include statement using absolute paths. Gromacs version is 5.0.

I also tried inserting the ions into a box with water using gmx genion. The
results are the same: Ion-Ion interactions are present and non-zero, but
Ion-SOL, SOL-SOL etc. are zero. The problem arises using various temperature
and pressure coupling algorithms. Apart from that, the simulations seem to
run smoothly and not doing exceptionally weird things, even reproduce
results.

I am unable to grasp the source of the issue here, so if you can help, any
input is welcome. Presumably it's just a mistake regarding input on my part,
but I have been trying to solve this problem for quite some time now, so I'm
writing to the mailing list.

Thanks in advance and kind regards,
Julian Michalowsky
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[gmx-users] GPU suggestions

[Eric Smoll]

Hello Gromacs users,

We are running GROMACS molecular dynamics simulations on a cluster with the
following specs: supermicro hardware, sandy bridge and haswell intel Xeons,
4 GB per core, Mellanox 10 GbE (w/RDMA) switching (no IB).

We were thinking of adding GPU's to this system. Does anyone have any
suggestions or advice?

Best,
Eric
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Re: [gmx-users] Efficiently running multiple simulations

[Mark Abraham]

Hi,

On Thu, Sep 17, 2015 at 6:24 PM Zimmerman, Maxwell 
wrote:

> Hi Mark,
>
> Thank you for reviewing the log files! I will recompile GROMACS for
> AVX2_256 SIMD to efficiently use the CPUs.
>
> The number of cores on the node is 16 and each core has two threads. By
> default, GROMACS picked 4 threads per simulation. I reran the simulation by
> specifying 2 threads per simulation and am providing a link to the new log
> file. I still see the same results, which is a lower performance per
> simulation when using 8 simulations on the node opposed to just 1.
>

OK. That's quite good evidence that (probably) your MPI system or job
scheduler is involving itself in the decision of how to lay out the 8 ranks
in a way that isn't working well. (The PME tuning is also still trying very
hard to shift workload off the CPU and onto the GPUs.)

For example, your MPI setup might put the 8 ranks on the first 8 cores, and
bind the ranks threads to those cores, and now the other 8 cores are unused
*and* the "second" OpenMP thread isn't getting great value if it has to be
the second thread on the same core. mpirun typically takes various options
to control how this works, so you should find out what default is working
for you (docs, sysadmins), and try some alternatives.

Since you have 16 real cores, you probably have 2 processor dies, each with
8 cores. You probably want 4 simulations per die, each with its threads on
adjacent cores. First, try each simulation with two OpenMP threads, so that
you have one single thread running per core. This should be a dramatic
performance improvement. Then try four OpenMP threads on those two cores,
which will probably improve things a bit further.

https://www.dropbox.com/s/rd3akpqcn3mo7c5/md_8GPUs_2Cores.log?dl=0
>
> My problem isn't that I am confusing "node" with "simulation", but rather
> that each of the 8 log files (each log file corresponds to a single
> simulation of the 8 that were run using "-multi") shows mapping to 8 GPUs.
> Is each log file telling me that the simulations are all aware of each
> other,


Yes. Each simulation is running on the same node, so each is reporting the
same properties about that node. mdrun -gpu_id maps PP ranks present on the
node to GPUs present on the node; in this case each PP rank comes from a
different simulation. The code that handles gmx mdrun_mpi -multi 8 knows
it's running 8 simulations, and observes they're all on the same node, so
it does the obvious thing.

or is each simulation trying to create 8 domains to split up on the GPUs?
>

No. Each log file clearly reports that its simulation has 1 MPI rank and
thus 1 domain. I've already said there's no way to split that 1 domain up.

Once you've got things working properly, you can experiment with mpirun -np
16 mdrun_mpi -multi 8 -gpu_id 0011223344556677 -ntomp 2 (or -ntomp 1) and
observe the difference in the log files.

I am still puzzled as to the loss in performance with increasing number of
> simulations on the node. I tried running 2 simulations with 2 GPUs and 4
> CPUs, 4 simulations with 4 GPUs and 8 CPUs, and 6 simulations with 6 GPUs
> and 12 CPUs. For the increasing number of simulations on the node, I see a
> greater loss in performance for individual simulations.
>

That's consistent with increasing contention for whatever subset of the CPU
cores is being used in practice. If you can log into the node
interactively, there are various performance monitoring tools that will
show you the occupancies of the CPU cores (and GPUs). Talk with your
sysadmins.

Mark


> Regards,
> -Maxwell
>
> ___
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Wednesday, September 16, 2015 4:44 PM
> To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Efficiently running multiple simulations
>
> Hi,
>
> The log files tell you that you should compile for AVX2_256 SIMD for the
> Haswell CPUs you have. Do that. Your runs are wasting a fair chunk of the
> value of the CPU hardware, and your setup absolutely needs to extract every
> last drop from the CPUs. That means you need to follow the instructions in
> the GROMACS install guide, which suggest you use a recent compiler. Your
> GROMACS was compiled with gcc 4.4.7, which was about two years old before a
> Haswell was sold! Why HPC clusters buy the latest hardware and continue to
> default to the "stable" 5-year old compiler suite shipped with the
> "enterprise" distribution remains a total mystery to me. :-)
>
> The log file also says that your MPI system is starting four OpenMP threads
> per rank in the multi-simulation case, so the comparison is not valid.
> Starting 8*4 OpenMP threads on your node oversubscribes the actual cores,
> and this is terrible for GROMACS. You need to find out how many actual
> cores you have (each of 

Re: [gmx-users] energygrps interactions are 0 for water

[Mark Abraham]

Hi,

You're probably running on GPUs, and have missed the note in the .log file
that observes that energy groups are not supported there (it'd be too slow
to run).

If you want such data, then the recommend procedure is to run your
simulation normally, then use gmx mdrun -rerun old-trajectory -nb cpu,
which does the energy decomposition you want.

Mark

On Thu, Sep 17, 2015 at 7:00 PM Julian Michalowsky 
wrote:

> Hi,
>
> I have a problem regarding the calculation of interaction energies using
> gmx energy and the energygrps parameter in the mdp file. My mdp file
> includes the line
>
> energygrps = Ion OW
>
> Whenever I calculate the LJ-SR and Coul.-SR energy terms between OW
> and any other energy group, the result is just zero. I am using an
> appropriate
> index file during preprocessing that defines OW as a group and also tried
> SOL and Water as energygrps in the mdp file.
>
> I originally used this with a custom force field, but encountered the same
> problem during a test run using the gromos54a7.ff from the default top
> directory.
>
> The system is a simple electrolyte solution (NaCl in water). I use a python
> script to set up the initial gro file. Ions are referred to as NA, CL in
> both gro
> and top file (not NA+ or CL-, if that makes any difference). The top file
> includes the respective forcefield.itp, ions.itp and spce.itp topologies
> via
> the #include statement using absolute paths. Gromacs version is 5.0.
>
> I also tried inserting the ions into a box with water using gmx genion. The
> results are the same: Ion-Ion interactions are present and non-zero, but
> Ion-SOL, SOL-SOL etc. are zero. The problem arises using various
> temperature
> and pressure coupling algorithms. Apart from that, the simulations seem to
> run smoothly and not doing exceptionally weird things, even reproduce
> results.
>
> I am unable to grasp the source of the issue here, so if you can help, any
> input is welcome. Presumably it's just a mistake regarding input on my
> part,
> but I have been trying to solve this problem for quite some time now, so
> I'm
> writing to the mailing list.
>
> Thanks in advance and kind regards,
> Julian Michalowsky
> --
> Gromacs Users mailing list
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> * Please search the archive at
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Re: [gmx-users] New atom definition

[Justin Lemkul]

On 9/17/15 3:08 PM, Maryam Kowsar wrote:

Dear all,

I want to use some atoms that are not implemented in gromacs. If i even
make a .gro file, making a topology is a problem. What should i do?



Derive parameters in a manner consistent with the desired force field and add 
all necessary bonded and nonbonded parameters to ffbonded.itp and ffnonbonded.itp.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] New atom definition

[Maryam Kowsar]

Dear all,

I want to use some atoms that are not implemented in gromacs. If i even
make a .gro file, making a topology is a problem. What should i do?

Thanks!
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Re: [gmx-users] Choose index group from terminal input.

[Dawid das]

Thank you.

2015-09-17 12:37 GMT+01:00 Mark Abraham :

> Hi,
>
> Yes. Further options at
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
> Mark
>
> On Thu, Sep 17, 2015 at 1:04 PM Dawid das  wrote:
>
> > O'right, I have figured that out myself. Just use text file like data.txt
> > with two lines:
> > 1
> > 1
> >
> > and redirect it: g_rms [options] < data.txt
> >
> > 2015-09-17 11:32 GMT+01:00 Dawid das :
> >
> > > Dear Gromacs Experts,
> > >
> > > Let's say that for some reasons I don't want to specify the atom group
> > > when g_rms (or other module) prompts me to do so.
> > > So I do not want to see this:
> > >
> > > Select group for RMSD calculation
> > > Group 0 ( System) has 38387 elements
> > > Group 1 (Protein) has  3470 elements
> > > Group 2 (  Protein-H) has  1772 elements
> > > Group 3 (C-alpha) has   217 elements
> > > Group 4 (   Backbone) has   653 elements
> > > Group 5 (  MainChain) has   869 elements
> > > Group 6 (   MainChain+Cb) has  1065 elements
> > > Group 7 (MainChain+H) has  1076 elements
> > > Group 8 (  SideChain) has  2394 elements
> > > Group 9 (SideChain-H) has   903 elements
> > > Group10 (Prot-Masses) has  3461 elements
> > > Group11 (non-Protein) has 34917 elements
> > > Group12 (  Water) has 34845 elements
> > > Group13 (SOL) has 34845 elements
> > > Group14 (  non-Water) has  3542 elements
> > > Group15 (Ion) has72 elements
> > > Group16 ( NA) has37 elements
> > > Group17 ( CL) has35 elements
> > > Group18 ( Water_and_ions) has 34917 elements
> > > Group19 (Chromophore) has37 elements
> > > Select a group: 1
> > > Selected 1: 'Protein'
> > >
> > > and I want to specify this Group 1 (Protein) in my command, e.g.
> > > g_rms -s ../npt-md2.tpr -f ../npt-md2.xtc -tu ns -b 0 -e 100 -n
> > > ../index.ndx -o rmsd-0-100.xvg
> > > -some_option 1
> > > Is it possible?
> > >
> > >
> > --
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Re: [gmx-users] Efficiently running multiple simulations

[Mark Abraham]

Hi,

That doesn't make any sense unless someone else is on your node :-)
Otherwise, maybe there's no pinning actually active? Try mpirun -np 8
mdrun_mpi -multi 8 -ntomp 1 -pin on -gpu_id 01234567 and look at the core
usage. There should be 8 empty cores and no movement between them.

Mark


>
> On Thu, Sep 17, 2015 at 9:41 PM Zimmerman, Maxwell 
> wrote:
>
>>
>> Hi Mark,
>>
>> I am not sure that there is a problem with the MPI system or job
>> scheduler. When I run 8 simulations with 2 threads and log onto the node, I
>> can see that every core is being used equally.
>>
>> Regards,
>> -Maxwell
>>
>>
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Re: [gmx-users] New atom definition

[Maryam Kowsar]

Thaks justin!
I did it several times and it worked. But now when i want to add some
neutral gas or heavy atoms it stops me with the error that the atom is not
defined. I dont know where i make a mistake.

On Friday, September 18, 2015, Justin Lemkul  wrote:

>
>
> On 9/17/15 3:08 PM, Maryam Kowsar wrote:
>
>> Dear all,
>>
>> I want to use some atoms that are not implemented in gromacs. If i even
>> make a .gro file, making a topology is a problem. What should i do?
>>
>>
> Derive parameters in a manner consistent with the desired force field and
> add all necessary bonded and nonbonded parameters to ffbonded.itp and
> ffnonbonded.itp.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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[gmx-users] REMD and distance restraints problem in gmx 4.6.7

[Christopher Neale]

Dear Users:

I have a system with many distance restraints, designed to maintain helical 
character, e.g.:
[ distance_restraints ]
90 33 1 1 2 2.745541e-01 3.122595e-01 999 1.0
97 57 1 2 2 2.876300e-01 2.892921e-01 999 1.0
114 73 1 3 2 2.704403e-01 2.929642e-01 999 1.0
...

Distance restraints are properly turned on in the .mdp file with:
disre=simple
disre-fc=1000

The run works fine on a single node (gmx 4.6.7 here and for all that follows):
mdrun -nt 24 ...

The run also works fine on two nodes:
ibrun -np 48 mdrun_mpi ...

However, if I try to do temperature replica exchange (REMD), with two replicas 
and two nodes like this:
ibrun -np 48 mdrun_mpi -multi 2 -replex 200 ...

then I get the error message:
Fatal error:
Time or ensemble averaged or multiple pair distance restraints do not work 
(yet) with domain decomposition, use particle decomposition (mdrun option -pd)

Aside: I tried particle decomposition, but when I do that without the REMD, 
simply running the 48-core job that worked fine with domain decomposition, I 
get LINCS errors and quickly a crash (note that without -pd I have 25 ns and 
counting of run without error):
Step 0, time 0 (ps)  LINCS WARNING in simulation 0
relative constraint deviation after LINCS:
rms 5.774043, max 48.082966 (between atoms 21554 and 21555)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
...

So I am stuck with an error message that is not entirely helpful because (a) 
the -pd option does not solve the issue even without REMD and also (b) the 
issue seems to be related to REMD (because without REMD I can run on multiple 
nodes) though that is not mentioned in the error message.

I note that Mark Abraham mentioned here: http://redmine.gromacs.org/issues/1117 
that:
"You can use MPI, you just can't have more than one domain (= MPI rank) per 
simulation. For a multi-simulation with distance restraints and not 
replica-exchange, you thus must have as many MPI ranks as simulations, so that 
each simulation has one rank and thus one domain."

I have trouble interpreting this, as I have always thought that running MPI 
across multiple nodes requires multiple domains (apparently = MPI ranks), so I 
am confused as to why that is possible without REMD but gets messy with REMD.

Final note: I am not trying to do "Time or ensemble averaged" distance 
restraints, and I think that I am not trying to do "multiple pair distance 
restraints", unless that simply means having more than one  simple distance 
restraint. So at the very least I think that the error message that I get is 
confusing.

If the solution or source of error is obvious then sorry.. maybe I just don't 
get MPI well enough.

Thank you for your suggestions,
Chris.

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