Re: [gmx-users] Simulating different pH values of water

[Kester Wong]

Hi Tsjerk,Thanks for your reply. I want to study the effect of pH on the wetting behaviour of water nanodroplet on graphene, the contact angle especially.For acidic solution, H and Cl ions are included in the water model, whereas for a high pH solution, there will be Na and OH ions, for instance.I am aware that a lot of quantum mechanics studies have been put into obtaining the H2O-carbon interaction properties with MP2 level accuracy.Using polarisable force field in this case might capture the properties of the charged ions, however, I am concerned if this approach is appropriate.Any feedback is greatly appreciated.Regards,Kester- 원본 메일 -보낸사람 : Tsjerk Wassenaar tsje...@gmail.com받는사람 : Discussion list for GROMACS us gmx-us...@gromacs.org받은날짜 : 2014년 8월 21일(목) 14:37:55제목 : Re: [gmx-users] Simulating different pH values of waterHi Kester,

You do realize that water is odd quantum stuff, with oxygens going about in
a sea of protons? The main way to move a free proton is to rewire the O-H
bonds. What effects do you want investigate with your simulations? That
determines what setup you need.

Cheers,

Tsjerk
On Aug 21, 2014 6:46 AM, "Kester Wong"  wrote:

 Dear all,


 This might not be relevant to MD technicalities, but I guess I should give
 it a shot.


 I would like to simulate water droplets at different pH values.

 However, knowing that a realistic system would need 180k water molecules
 to mimic a pH of 7.

 Is there another viable approach that I can use to simulate water droplets
 from low to high pH values?


 The original question was posted here:


 https://www.researchgate.net/post/How_can_I_calculate_the_number_of_molecules_with_respect_to_the_pH-value_in_solution?_tpcectx=subscription_feed#53f576d7d4c11805568b469c



 Regards,

 Kester

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[gmx-users] Error using pdb2gmx tool

[ankit agrawal]

hi,
I was simulating A cadherin molecule (PDB ID: 4APX). I removed all the
water molecule from molecule then ran the following command.

pdb2gmx -f 4APX.pdb -water tip3p

then I chose force field : CHARMM27 (with CMAP) after that it should create
3 types of files  (.gro, .itp, .top) but it is not generating the .gro file
and showing an error.
Fatal error: Residue 'CA' not found in residue topology database.

Please help me to solve this error.
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Re: [gmx-users] CUDA5.5 and ICC 14

[Theodore Si]

Thanks!

On 8/20/2014 8:03 PM, Mark Abraham wrote:

Hi,

Per Nvidia's docs and that error, CUDA 5.5 is only supported with that icc
version. In practice, I understand that other icc versions work fine with
GROMACS, but you would need to go and comment out that #error message.
Alternatively, CUDA 6.5 supports icc 14.0 (only).

Mark


On Wed, Aug 20, 2014 at 8:26 AM, Theodore Si sjyz...@gmail.com wrote:


Hi,

I am using CUDA 5.5 and Intel ICC 14.0.1 to compile GROMACS and this
happened:

[  0%] Building NVCC (Device) object src/gromacs/gmxlib/gpu_utils/
CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
In file included from /usr/local/cuda-5.5/include/cuda_runtime.h(59),
  from /home/theo/gromacs-5.0/src/gromacs/gmxlib/gpu_utils/
gpu_utils.cu(0):
/usr/local/cuda-5.5/include/host_config.h(72): catastrophic error: #error
directive: -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64
is supported!
   #error -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64
is supported!
^

CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message):
   Error generating
/home/theo/gromacs-5.0/build/src/gromacs/gmxlib/gpu_utils/
CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o


make[2]: *** [src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./
gpu_utils_generated_gpu_utils.cu.o] Error 1
make[1]: *** [src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all]
Error 2
make: *** [all] Error 2

Does this mean that I cannot make them work together?

BR,
Theo
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Re: [gmx-users] Install errors

[Valentina Loconte]

Thanks!


2014-08-20 14:05 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com:

 Hi,

 You should be using a supported host compiler for your version of CUDA
 (check its docs, probably gcc 4.7 or 4.8, for example), rather than clang.

 Mark


 On Wed, Aug 20, 2014 at 9:59 AM, Valentina Loconte 
 valentina.loco...@studenti.unipd.it wrote:

  Hi,
  I'm trying to install the gromacs version 4.6.5. with the Quick and
 dirty
  installation. When I give the command make the platform gives me back
 this
  message of error:
 
   clang: error: unsupported option '-dumpspecs'
 
  clang: error: no input files
 
  CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:206
  (message):
 
Error generating
 
 
 
 
 /Users/Valentina/Software/gromacs-4.6.6/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o
 
 
 
  make[2]: ***
 
 
 [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_memtestG80_core.cu.o]
  Error 1
 
  make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2
 
  make: *** [all] Error 2
 
  How may I avoid this problem?
 
  Thanks,
 
  Valentina
 
  --
  Valentina Loconte, PhD student
  Department of Biomedical Sciences
  University of Padova
  Viale G. Colombo 3
  35131 Padova, Italy
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-- 
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Department of Biomedical Sciences
University of Padova
Viale G. Colombo 3
35131 Padova, Italy
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Re: [gmx-users] Error using pdb2gmx tool

[Justin Lemkul]

On 8/21/14, 5:24 AM, ankit agrawal wrote:

hi,
I was simulating A cadherin molecule (PDB ID: 4APX). I removed all the
water molecule from molecule then ran the following command.

pdb2gmx -f 4APX.pdb -water tip3p

then I chose force field : CHARMM27 (with CMAP) after that it should create
3 types of files  (.gro, .itp, .top) but it is not generating the .gro file
and showing an error.
Fatal error: Residue 'CA' not found in residue topology database.



Calcium ions are called CAL in CHARMM.  Rename the residue(s) in the .pdb 
file.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Forcefield parameters for Zinc and phosphorylated residues

[Piggot T.]

Hi,

QM parameterisation is how people tend to have done it for things like 
copper-bound proteins with GROMOS. I have been recently simulating one of these 
copper-bound proteins using a GROMOS force field (and indeed an AMBER force 
field too). I can send you a couple of papers regarding the GROMOS 
parameterisation for this protein off list if you like, so you can at least see 
their parameterisation methods for the copper centre?

Cheers

Tom

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Michael Carter 
[michael.car...@icr.ac.uk]
Sent: 21 August 2014 13:10
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated 
residues

Hi Tom,

Thanks, I will look into it.

I know AMBER has the ZAFF forcefield, and I have done the simulation in AMBER, 
but I wanted to know if GROMOS forcefields have this capability. I will have a 
play and see what I can do, most likely I will do a small QM/MM run and use 
this to parameterise the Zinc ions.

Thanks for the help.

Cheers,
Mike

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Piggot T. 
[t.pig...@soton.ac.uk]
Sent: Wednesday, August 20, 2014 4:46 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated 
residues

Hi Mike,

As well as the link that Bipin sent, you can also get parameters for GROMOS 
phosphorylated residues (compatible with the 43A1 force field, I think) from:

http://www.gromacs.org/Downloads/User_contributions/Force_fields

I've never used either so have no idea which might be better. The ones that 
Binpin suggested look like they work with the newer GROMOS 54A7 force field, so 
they might be the ones to use.

On your other question, I am not sure about the protein-zinc parameters with a 
GROMOS force field. I would say, is there any particular need for using one of 
the GROMOS protein force fields? There are definitely parameters out there for 
some of the all-atom protein force fields (e.g. AMBER ones) which are probably 
also better in terms of protein parameters.

Cheers

Tom

PS: Hope things are good in the (relatively) new job!

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Michael Carter 
[michael.car...@icr.ac.uk]
Sent: 20 August 2014 12:56
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated 
residues

Hi Bipin,

Thanks for this. It works well for adding functionality to residues.

Cheers,
Mike Carter


On 20/08/2014 12:10, bipin singh bipinel...@gmail.com wrote:

This might help.

http://vienna-ptm.univie.ac.at/



*Thanks and Regards,Bipin Singh*



On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter michael.car...@icr.ac.uk
wrote:

 Hi,

 I have two questions regarding the parameterisation of Zinc ions and a
 phosphorylated TYR residue within two different protein systems.


  1.  Zinc parameters:

 I have three zinc ions within one protein system. I want to use a bonded
 model so that they do not fly out of my protein upon simulation. Is
there
 any documentation on the parameters for such a model in the GROMOS
 forcefield?

 2. Phosphorylated TYR

 In another system I have a phosphorylated TYR residue. PDB2GMX does not
 like this and after looking inot the manual I have found that you can
add
 parameters for this to the existing forcefields. Much like the previous
 question, is there any documentation on the addition of parameters for
 phosphorylated residues in the GROMOS forcefield?

 Any pointers for these questions would be greatly appreciated.

 Cheers,
 Mike Carter

 The Institute of Cancer Research: Royal Cancer Hospital, a charitable
 Company Limited by Guarantee, Registered in England under Company No.
 534147 with its Registered Office at 123 Old Brompton Road, London SW7
3RP.

 This e-mail message is confidential and for use by the addressee only.
If
 the message is received by anyone other than the addressee, please
return
 the message to the sender by replying to it and then delete the message
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[gmx-users] How invoke hamiltonian replica exchange in 4.6.5

[jia jia]

Dear gmx users:
  I got a problem that I could not invoke hamiltonian replica exchange in
version 4.6.5. I've different lambda value for each replica (
free_energy  = yes; init-lambda =  0.X  ) however I got error the
properties of the 4 systems arre all the same...
  I've tried the method suggested in
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083425.html
, however after add fep-lambdas  =  0.X I still get same error.
  I'm checking src/kernel/repl_ex.c and found if my systems are assigned to
hamiltonian replica exchange,  it should report Replica exchange in
lambda to log file ( around l299), and in my log file it has Replica
exchange in temperature so it shows I failed at invoke  hamiltonian
replica exchange.
  I just wonder would any one like to tell me how to invoke hamiltonian
replica exchange in 4.6.5 (or other 4.6 version)?
Thank you!
Yours
Guang
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Re: [gmx-users] Several questions about log file.

[Mark Abraham]

On Thu, Aug 21, 2014 at 7:57 AM, Theodore Si sjyz...@gmail.com wrote:

 Hi,

 1. Does force in the R E A L   C Y C L E   A N D   T I M E   A C C O U N
 T I N G table mean the time spent on short-range force calculation?


and bonded interactions.


 2. Does Comm. coord mean the communication of atom positions when
 calculating short-range force interaction?


As I've said before, the entries in this table correspond to sections in
the DD-PME flowchart in figure 3.16 of the manual. It's not 1-to-1, but the
correspondence is fairly clear. As you can see there, there can be two
kinds of communication of position coordinates required. So the answer to
your question is yes but there can be more to it.


 3. What forces are waited and communicated in Wait + Comm. F?


Real-space forces from DD neighbours, per flowchart.


 Each node of our cluster has two Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz,
 each has 8 cores.

 When we are using 2 nodes, that is 2nodes * 2 cpus * 8 cores = 32 cores,
 we will be
 Using 32 MPI processes
 Using 1 OpenMP thread per MPI proces
 and
 Comm. coord.  241  19200   1.483 92.327 1.0
 1.483s are spent on the coordinate communication


 When we are using 32 nodes, that is 32nodes * 2 cpus * 8 cores = 32 cores,
 we will be
 Using 512 MPI processes
 Using 1 OpenMP thread per MPI proces
 and
 Comm. coord. 3841  19200   2.094 2086.377 5.2
 2.094s are spent on the coordinate communication

 4. Why the time spent on communication of coordinate doesn't scale up as
 the cores are increasing


Someone coded it right ;-) The implementation is talked about in manual
3.17.1. The total volume of communication does increase as there are more
domains(=ranks), but only communication between different nodes will have
an effect (to first order). The actual performance properties will depend
on the qualities of your network, but the total amount of coordinate data
transferred (three 4-byte floats per ~100 atoms per domain-pair) is tiny
compared with what typical networks are designed to handle, so the total
cost of the communication will be dominated by the latency of just sending
a message. The number of domain-pairs sending messages has gone up, of
course, but your results show that the cost is still dominated by latency
(which is not news, of course, hiding such latencies is key for improving
strong scaling of MD).

Mark


 BR,
 Theo

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Re: [gmx-users] REMD tutorial

[Mark Abraham]

On Thu, Aug 21, 2014 at 8:01 AM, shahab shariati shahab.shari...@gmail.com
wrote:

 Dear Mark

 Before, in following address you said: Google knows about two GROMACS REMD
 tutorials.


 https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-January/086563.html

 Unfortunately, I could not find tutorials you mentioned.


You can find them here
https://www.google.se/search?q=gromacs+remd+tutorialsoq=gromacs+remd+tutorials



 

 Also, in following address you said: I've added a section on
 replica-exchange to
 http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation


 https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2007-December/031188.html
 .

 Is this link active, now? I have no access to this link.


The webpage has been changed since then, see link from
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation

Mark



 -

 I want to know Is there a tutorial for REMD like what is in
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/.

 Any help will highly appreciated.
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Re: [gmx-users] How invoke hamiltonian replica exchange in 4.6.5

[Mark Abraham]

Are your temperatures the same in each replica?

Mark


On Thu, Aug 21, 2014 at 4:08 PM, jia jia jzg...@gmail.com wrote:

 Dear gmx users:
   I got a problem that I could not invoke hamiltonian replica exchange in
 version 4.6.5. I've different lambda value for each replica (
 free_energy  = yes; init-lambda =  0.X  ) however I got error the
 properties of the 4 systems arre all the same...
   I've tried the method suggested in

 https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083425.html
 , however after add fep-lambdas  =  0.X I still get same error.
   I'm checking src/kernel/repl_ex.c and found if my systems are assigned to
 hamiltonian replica exchange,  it should report Replica exchange in
 lambda to log file ( around l299), and in my log file it has Replica
 exchange in temperature so it shows I failed at invoke  hamiltonian
 replica exchange.
   I just wonder would any one like to tell me how to invoke hamiltonian
 replica exchange in 4.6.5 (or other 4.6 version)?
 Thank you!
 Yours
 Guang
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[gmx-users] regarding MSD

[Nidhi Katyal]

Hello all

I have read few papers that determine transition temperature from the plot
of average MSD versus temperature. My question is:
At a particular temperature, we get a linear curve for MSD versus time, is
it reasonable to calculate average MSD over all such time points? Is this
the average that is plotted in papers (or something is missing) ? My doubt
is won't this average depend on the number of time points (due to its
linear nature)?
Any help is highly appreciated.

Thanks
Nidhi
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Re: [gmx-users] Extending simulation problem.

[Dawid das]

Well in my *log file nothing about state or *cpi files is mentioned.
Acutally I have a question regarding state.cpi files. Does it contain names
of *gro, *trr, etc. files if they are not standard?
The thing is, that output files from my first 5ns simulation are not
standard. Now, I perform these calculations not in my working directory but
on separate scratch.
In this case, should the output files from previous simulation be present
in the scratch?
And when I run another 5 ns should I run mdrun with those -c -o and -e
options? If yes, should the names of files be the same as in the previous
simulation?


2014-08-20 18:18 GMT+01:00 Justin Lemkul jalem...@vt.edu:



 On 8/20/14, 6:33 AM, Dawid das wrote:

 Dear Gromacs experts,

 I googled for answer and I found these:
 http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
 http://www.researchgate.net/post/How_to_extend_the_
 protein_simulation_in_Gromacs_from_1000_ps_to_1_ps

 but still I am confused about what happens in my simulation. I did 5 ns
 simulation and I would like to add extra 5 ns on top of that so that new
 results (energies, temperature, trajectory, etc.) will be appended to
 already existing files after first 5 ns simulation. Now I used this
 command
 to run MD simulation for the first time:

 \$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro -e
 mCherry7-npt-md.edr  $CURDIR/mCherry7-npt-md.log 21

 After this in the same directory I run:

 tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr
 \$MDRUN -s npt-md-ext.tpr -cpi state.cpt

 I tried both state.cpt and prev_state.cpt and the beginning of new
 simulation looks exactly the same

 that means temperature, energies, etc. are the same as if I started
 from 0ns step, not from 5ns step of

 previous simulation. What can cause that? Is it because of used files
 names or I did something else wrong?


 What does the .log file say?  It should clearly indicate if the restart
 was done by reading in the checkpoint file.

 -Justin

 --
 ==

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

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 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] Numerical Stability of Gromacs Implementation

[Johnny Lu]

Sorry for asking this. Is it possible for me to get some references about
the claims of instability of gromacs simulations, and their debunk?

From the few papers that I read, I guess algorithms of molecular dynamics
do not treat all observables equally well.
Some old papers say that the velocity in velocity verlet is not symplectic,
but rather follows some shadow hamiltonian or generalized equipartition
theorem.
Then another one mentioned force splitting can reduce the resonance effect
caused by integrator.
That said, very few papers talk about this.

I don't know much about the effect of MD on the observables that I try to
look at.
And, sorry for replying this late, I have been installing gromacs on aix
for a week.
Compiling gcc took 3 days of computer time.


On Thu, Aug 14, 2014 at 2:29 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 On Wed, Aug 13, 2014 at 1:19 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  Hi again.
 
  Some of my friends said that gromacs had lower numerical stability than
  amber, and occasionally has mysterious error in energy.
 

 Show us a result and we'll discuss fixing it ;-)


  Is that still true? Does the implementation of Integrator cause more
  resonance effect?
 

 Any numerical software can be used poorly. Any numerical software can have
 bugs. Give them the same input to two implementations of the same algorithm
 and they should give results that are similar (whatever that means in the
 problem domain).


  I am trying to run NVE simulation with the single precision version, and
 so
  I guess the implementation of thermostats is not my most immediate
 concern
  at the moment.
 
  I searched online, and haven't found much about numerical instability of
  gromacs using amber forcefield (I mean for version 4.6, which supports
 the
  amber force-fields without modification.)
 

 What do you mean by numerical stability? Should you actually be concerned
 about getting a correct physical observable? People look at energy
 conservation because it is easy to do, but connecting that to the quality
 of the resulting physics is non-trivial. Even if you can (say) deliver
 state-of-the-art energy conservation (and most packages can do this in some
 mode), you still need to measure the price in simulation throughput
 incurred by running in that mode. The overall objective is to deliver
 science of sufficient quality with minimal time to solution. In some cases,
 it is right to let some energy leak and let the thermostat fix it, if you
 generate many more samples by so doing.

 Why do people still use and paid for amber, when gromacs is free?
  I look online and the number of papers that use amber is about twice of
 the
  number of paper that use gromacs. There are very few papers that
 mentioned
  both gromacs and amber.
 

 Inertia is a big effect. You tend to adopt the package used by the local MD
 expert so you have a low-latency person of whom to ask questions. They tend
 to still use the package they used in their doctoral work, regardless of
 current technical merit, because learning to use such software well is
 tricky and discarding your old workflows is not a cheap proposition. The
 next biggest effect is what functionality is available, and at what
 performance.

 Mark

 Thank you.
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Re: [gmx-users] [gmx-developers] About dynamics loading balance

[Roland Schulz]

Hi,


On Thu, Aug 21, 2014 at 1:56 PM, Yunlong Liu yliu...@jh.edu wrote:

  Hi Roland,

 The problem I am posting is caused by trivial errors (like not enough
 memory) and I think it should be a real bug inside the gromacs-GPU support
 code.

It is unlikely a trivial error because otherwise someone else would have
noticed. You could try the release-5-0 branch from git, but I'm not aware
of any bugfixes related to memory allocation.
The memory allocation which causes the error isn't the problem. The printed
size is reasonable. You could recompile with PRINT_ALLOC_KB (add
-DPRINT_ALLOC_KB to CMAKE_C_FLAGS) and rerun the simulation. It might tell
you where the usual large memory allocation happens.

PS: Please don't reply to an individual Gromacs developer. Keep all
conversation on the gmx-users list.

Roland



 That is the reason why I post this problem to the developer mailing-list.

 My system contains ~240,000 atoms. It is a rather big protein. The memory
 information of the node is :

 top - 12:46:59 up 15 days, 22:18,  1 user,  load average: 1.13, 6.27, 11.28
 Tasks: 510 total,   2 running, 508 sleeping,   0 stopped,   0 zombie
 Cpu(s):  6.3%us,  0.0%sy,  0.0%ni, 93.7%id,  0.0%wa,  0.0%hi,  0.0%si,
 0.0%st
 Mem:  32815324k total,  4983916k used, 27831408k free, 7984k buffers
 Swap:  4194296k total,0k used,  4194296k free,   700588k cached

 I am running the simulation on 2 nodes, 4 MPI ranks and each rank with 8
 OPENMP-threads. I list the information of their CPU and GPU here:

 c442-702.stampede(1)$ nvidia-smi
 Thu Aug 21 12:46:17 2014
 +--+

 | NVIDIA-SMI 331.67 Driver Version: 331.67
 |

 |---+--+--+
 | GPU  NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr.
 ECC |
 | Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute
 M. |

 |===+==+==|
 |   0  Tesla K20m  Off  | :03:00.0 Off
 |0 |
 | N/A   22CP046W / 225W |172MiB /  4799MiB |  0%
 Default |

 +---+--+--+



 +-+
 | Compute processes:   GPU
 Memory |
 |  GPU   PID  Process name
 Usage  |

 |=|
 |0113588  /work/03002/yliu120/gromacs-5/bin/mdrun_mpi
 77MiB |
 |0113589  /work/03002/yliu120/gromacs-5/bin/mdrun_mpi
 77MiB |

 +-+

 c442-702.stampede(4)$ lscpu
 Architecture:  x86_64
 CPU op-mode(s):32-bit, 64-bit
 Byte Order:Little Endian
 CPU(s):16
 On-line CPU(s) list:   0-15
 Thread(s) per core:1
 Core(s) per socket:8
 Socket(s): 2
 NUMA node(s):  2
 Vendor ID: GenuineIntel
 CPU family:6
 Model: 45
 Stepping:  7
 CPU MHz:   2701.000
 BogoMIPS:  5399.22
 Virtualization:VT-x
 L1d cache: 32K
 L1i cache: 32K
 L2 cache:  256K
 L3 cache:  20480K
 NUMA node0 CPU(s): 0-7
 NUMA node1 CPU(s): 8-15

 I hope this information will help. Thank you.

 Yunlong






 On 8/21/14, 1:38 PM, Roland Schulz wrote:

 Hi,

  please don't use gmx-developers for user questions. Feel free to use it
 if you want to fix the problem, and have questions about implementation
 details.

  Please provide more details: How large is your system? How much memory
 does a node have? On how many nodes do you try to run? How many mpi-ranks
 do you have per node?

  Roland

 On Thu, Aug 21, 2014 at 12:21 PM, Yunlong Liu yliu...@jh.edu wrote:

 Hi Gromacs Developers,

 I found something about the dynamic loading balance really interesting. I
 am running my simulation on Stampede supercomputer, which has nodes with
 16-physical core ( really 16 Intel Xeon cores on one node ) and an NVIDIA
 Tesla K20m GPU associated.

 When I am using only the CPUs, I turned on dynamic loading balance by
 -dlb yes. And it seems to work really good, and the loading imbalance is
 only 1~2%. This really helps improve the performance by 5~7%。But when I am
 running my code on GPU-CPU hybrid ( GPU node, 16-cpu and 1 GPU), the
 dynamic loading balance kicked in since the imbalance goes up to ~50%
 instantly after loading. Then the the system reports a
 fail-to-allocate-memory error:

 NOTE: Turning on dynamic load balancing


 ---
 Program mdrun_mpi, VERSION 5.0
 Source code file:
 /home1/03002/yliu120/build/gromacs-5.0/src/gromacs/utility/smalloc.c, line:
 226

 Fatal error:
 Not enough memory. Failed to realloc 

[gmx-users] GROMACS version 5.0 incompatible with my hardware - help req

[Agnivo Gosai]

Dear Users

I initially installed GROMACS 5.0 in my office computer and tried running a
few sample tutorials over there.

It was showing a illegal instruction : core dumped error. On searching
the archived files in the user group I found that the version of GROMACS
installed in my computer is not compatible with the hardware.

So I have uninstalled all the GROMACS files one by one using the command :
sudo rm -rf /usr/bin/gromacs command

My computer hardware configuration is : - (A) Intel Core 2 CPU 6600 @ 2.40
GHz x 2
(B) 2.0 GB RAM DDR2
My OS is ubuntu 14.04 LTS 64-Bit

Could anyone please tell me what version of GROMACS I should try installing
??

Thanks  Regards

Agnivo Gosai
Graduate Student
Mechanical Engineering
Iowa State University
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Re: [gmx-users] GROMACS version 5.0 incompatible with my hardware - help req

[Johnny Lu]

where did you get gromacs?
how did you install it? (like you compile it yourself, or you get the
package with apt-get?)



On Thu, Aug 21, 2014 at 3:11 PM, Agnivo Gosai agnivo2...@gmail.com wrote:

 Dear Users

 I initially installed GROMACS 5.0 in my office computer and tried running a
 few sample tutorials over there.

 It was showing a illegal instruction : core dumped error. On searching
 the archived files in the user group I found that the version of GROMACS
 installed in my computer is not compatible with the hardware.

 So I have uninstalled all the GROMACS files one by one using the command :
 sudo rm -rf /usr/bin/gromacs command

 My computer hardware configuration is : - (A) Intel Core 2 CPU 6600 @ 2.40
 GHz x 2
 (B) 2.0 GB RAM DDR2
 My OS is ubuntu 14.04 LTS 64-Bit

 Could anyone please tell me what version of GROMACS I should try installing
 ??

 Thanks  Regards

 Agnivo Gosai
 Graduate Student
 Mechanical Engineering
 Iowa State University
 --
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Re: [gmx-users] GROMACS version 5.0 incompatible with my hardware - help req

[Johnny Lu]

or.. you get it from some rpm/deb binary file that is for another kind of
cpu?


On Thu, Aug 21, 2014 at 3:44 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 where did you get gromacs?
 how did you install it? (like you compile it yourself, or you get the
 package with apt-get?)



 On Thu, Aug 21, 2014 at 3:11 PM, Agnivo Gosai agnivo2...@gmail.com
 wrote:

 Dear Users

 I initially installed GROMACS 5.0 in my office computer and tried running
 a
 few sample tutorials over there.

 It was showing a illegal instruction : core dumped error. On searching
 the archived files in the user group I found that the version of GROMACS
 installed in my computer is not compatible with the hardware.

 So I have uninstalled all the GROMACS files one by one using the command :
 sudo rm -rf /usr/bin/gromacs command

 My computer hardware configuration is : - (A) Intel Core 2 CPU 6600 @ 2.40
 GHz x 2
 (B) 2.0 GB RAM DDR2
 My OS is ubuntu 14.04 LTS 64-Bit

 Could anyone please tell me what version of GROMACS I should try
 installing
 ??

 Thanks  Regards

 Agnivo Gosai
 Graduate Student
 Mechanical Engineering
 Iowa State University
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Re: [gmx-users] GROMACS version 5.0 incompatible with my hardware - help req

[Justin Lemkul]

On 8/21/14, 3:11 PM, Agnivo Gosai wrote:

Dear Users

I initially installed GROMACS 5.0 in my office computer and tried running a
few sample tutorials over there.

It was showing a illegal instruction : core dumped error. On searching
the archived files in the user group I found that the version of GROMACS
installed in my computer is not compatible with the hardware.



It's not the version of Gromacs, per se, it's the level of optimization.


So I have uninstalled all the GROMACS files one by one using the command :
sudo rm -rf /usr/bin/gromacs command

My computer hardware configuration is : - (A) Intel Core 2 CPU 6600 @ 2.40
GHz x 2
(B) 2.0 GB RAM DDR2
My OS is ubuntu 14.04 LTS 64-Bit

Could anyone please tell me what version of GROMACS I should try installing
??



What level of optimization (GMX_SIMD during cmake) was set before?  What does 
cmake detect on its own if GMX_SIMD is not explicitly set?  What compilers (and 
versions) are you using to compile?


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] pressure after NPT

[ibrahim khalil]

dear gromacs users, I am simulating Carbon nanotubes in water. I did the
NPT simulation with a reference pressure of 1 bar.

When I do an NPT simulation for about 100 ps, the system shows an average
pressure of 1.4 bar. So i thought a longer NPT simulation would give me a
better average pressure. But when i did an NPT for 200ps, the average
pressure was increased to 1.85 bar.

what can I do to improve my average pressure conditions?
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Re: [gmx-users] pressure after NPT

[Justin Lemkul]

On 8/21/14, 4:22 PM, ibrahim khalil wrote:

dear gromacs users, I am simulating Carbon nanotubes in water. I did the
NPT simulation with a reference pressure of 1 bar.

When I do an NPT simulation for about 100 ps, the system shows an average
pressure of 1.4 bar. So i thought a longer NPT simulation would give me a
better average pressure. But when i did an NPT for 200ps, the average
pressure was increased to 1.85 bar.

what can I do to improve my average pressure conditions?



http://www.gromacs.org/Documentation/Terminology/Pressure

A few hundred ps is very little in terms of getting pressure to stabilize, but 
likely the differences you observe from the target value are not meaningful.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Numerical Stability of Gromacs Implementation

[Mark Abraham]

On Thu, Aug 21, 2014 at 7:59 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 Sorry for asking this. Is it possible for me to get some references about
 the claims of instability of gromacs simulations, and their debunk?


Not really. You can find a paper from some of the Desmond authors that
correctly observes some issues in GROMACS 3.x. People occasionally refer to
it here as if it is current news. These issues are long fixed, but not
worth writing about - journal articles should be about delivering quality
science. More commonly, an issue would be handled via private email, though
even these are rare. Overall, the biomolecular MD community is quite good
at finding problems with their own and each other's algorithms and
implementations and getting them fixed constructively. People saying
someone said x was bad but gave me no details need to talk to the
someone, not just the authors of x ;-) If people start being evasive or
secretive about possible problems with their code... be concerned.

From the few papers that I read, I guess algorithms of molecular dynamics
 do not treat all observables equally well.
 Some old papers say that the velocity in velocity verlet is not symplectic,
 but rather follows some shadow hamiltonian or generalized equipartition

theorem.


This is common to all methods with a finite time step - see
http://en.wikipedia.org/wiki/Energy_drift. There are certainly a variety of
ways of estimating the velocity with common integrators, and they have
different quality attributes. You can read about how GROMACS handles this
in the manual.

Then another one mentioned force splitting can reduce the resonance effect
 caused by integrator.
 That said, very few papers talk about this.


There are lots of papers that discuss details of multiple time-stepping
algorithms that seek to deal with this issue directly.

 I don't know much about the effect of MD on the observables that I try to
 look at.


It's not an easy topic - generating converged sampling to assess whether an
integration scheme correctly samples a complex observable is still a
non-trivial matter. That needs to happen before questions of how much
algorithmic energy drift is acceptable can be satisfactorily addressed.
Until then, claims of my energy conservation is better than yours need to
be considered alongside my number of independent converged-ensemble
samples is better than yours.

 And, sorry for replying this late, I have been installing gromacs on aix
 for a week.
 Compiling gcc took 3 days of computer time.


Seriously, don't bother. I don't think there is any system that would have
AIX, with no gcc package available, and which GROMACS 5.0 would run
decently on (which would require SIMD support, which currently means x86 or
BlueGene/Q). I'd guess your laptop will get equivalent performance.

Mark



 On Thu, Aug 14, 2014 at 2:29 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

  On Wed, Aug 13, 2014 at 1:19 PM, Johnny Lu johnny.lu...@gmail.com
 wrote:
 
   Hi again.
  
   Some of my friends said that gromacs had lower numerical stability than
   amber, and occasionally has mysterious error in energy.
  
 
  Show us a result and we'll discuss fixing it ;-)
 
 
   Is that still true? Does the implementation of Integrator cause more
   resonance effect?
  
 
  Any numerical software can be used poorly. Any numerical software can
 have
  bugs. Give them the same input to two implementations of the same
 algorithm
  and they should give results that are similar (whatever that means in the
  problem domain).
 
 
   I am trying to run NVE simulation with the single precision version,
 and
  so
   I guess the implementation of thermostats is not my most immediate
  concern
   at the moment.
  
   I searched online, and haven't found much about numerical instability
 of
   gromacs using amber forcefield (I mean for version 4.6, which supports
  the
   amber force-fields without modification.)
  
 
  What do you mean by numerical stability? Should you actually be concerned
  about getting a correct physical observable? People look at energy
  conservation because it is easy to do, but connecting that to the quality
  of the resulting physics is non-trivial. Even if you can (say) deliver
  state-of-the-art energy conservation (and most packages can do this in
 some
  mode), you still need to measure the price in simulation throughput
  incurred by running in that mode. The overall objective is to deliver
  science of sufficient quality with minimal time to solution. In some
 cases,
  it is right to let some energy leak and let the thermostat fix it, if you
  generate many more samples by so doing.
 
  Why do people still use and paid for amber, when gromacs is free?
   I look online and the number of papers that use amber is about twice of
  the
   number of paper that use gromacs. There are very few papers that
  mentioned
   both gromacs and amber.
  
 
  Inertia is a big effect. You tend to adopt the package used by the local
 MD
 

Re: [gmx-users] too many lincs warnings

[Meenakshi Rajput]

Thanks..
On Aug 20, 2014 1:29 PM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote:

 hello users
 I had done energy minimisation of protein-ligand complex and i got
 negative potential. Also the ligand was at right place after EM run but
 when I tried the positional restrained run, too many lincs warnings came
 and md run stopped suddenly. I am using charmm force field and mdp file
 settings for position restrined run are:-
 define= -DPOSRES; position restrain the protein
 ; Run parameters
 integrator= md; leap-frog integrator
 nsteps= 5; 2 * 5 = 100 ps
 dt= 0.002; 2 fs
 ; Output control
 nstxout= 500; save coordinates every 0.2 ps
 nstvout= 500; save velocities every 0.2 ps
 nstenergy= 500; save energies every 0.2 ps
 nstlog= 500; update log file every 0.2 ps
 ; Bond parameters
 continuation= yes; first dynamics run
 constraint_algorithm = lincs; holonomic constraints
 constraints= all-bonds; all bonds (even heavy atom-H bonds)
 constrained
 lincs_iter= 1; accuracy of LINCS
 lincs_order= 4; also related to accuracy
 ; Neighborsearching
 cutoff-scheme   = Verlet
 ns_type= grid; search neighboring grid cells
 nstlist= 10; 10 fs
 rlist= 1.2; short-range neighborlist cutoff (in nm)
 rcoulomb= 1.2; short-range electrostatic cutoff (in nm)
 rvdw= 1.2; short-range van der Waals cutoff (in nm)
 rvdw-switch = 1.0
 ; Electrostatics
 coulombtype= PME; Particle Mesh Ewald for long-range
 electrostatics
 pme_order= 4; cubic interpolation
 fourierspacing= 0.16; grid spacing for FFT
 ; Temperature coupling is on
 tcoupl= V-rescale; modified Berendsen thermostat
 tc-grps= Protein Non-Protein; two coupling groups - more
 accurate
 tau_t= 0.10.1; time constant, in ps
 ref_t= 300 300; reference temperature, one for each group,
 in K
 ; Pressure coupling is off
 pcoupl= no ; no pressure coupling in NVT
 ; Periodic boundary conditions
 pbc= xyz; 3-D PBC
 ; Dispersion correction
 DispCorr= EnerPres; account for cut-off vdW scheme
 ; Velocity generation
 gen_vel= yes; assign velocities from Maxwell distribution
 gen_temp= 300; temperature for Maxwell distribution
 gen_seed= -1; generate a random seed

 Please tell me if there is something wrong with mdp settings or is it some
 other problem?


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Re: [gmx-users] Job Submission script for Multiple nodes GPUs calculation

[Carsten Kutzner]

Hi,

On 22 Aug 2014, at 01:38, Xingcheng Lin linxingcheng50...@gmail.com wrote:

 Good afternoon,
 
 I am trying to use multiple nodes to do GPU simulation, each node has two
 GPUs and 12 CPUs mounted. Is there any submission script for doing that?
 
 For single node I used:
 
 mpiexec -np 2 mdrun_mpi -s run.tpr -cpi state.cpt -cpo state.cpt -noappend
 -gpu_id 01 -nb gpu -ntomp 6
 
 For 2 nodes I cannot use the script like
 
 mpiexec -np 4 mdrun_mpi -s run.tpr -cpi state.cpt -cpo state.cpt -noappend
 -gpu_id 0123 -nb gpu -ntomp 6
The -gpu_id string refers to the GPU id’s _per node_, so you should also
use -gpu_id 01 on two and more of these nodes.

Best,
  Carsten



 
 Any suggestion about what I should do?
 
 Thank you,
 
 Arrow
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

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Re: [gmx-users] Interteting flooding results

[Carsten Kutzner]

Hi,

On 21 Aug 2014, at 23:27, Ricardo O. S. Soares rsoa...@fcfrp.usp.br wrote:

 Dear users, 
 
 could anyone give me some general guidelines or links to help me interpret 
 the essential dynamics/flooding output xvg file from a flooding simulation? 
That depends a bit on which Gromacs Version you are using. If you are using
a 4.6 or later version, look in the header of the .xvg file, there should be
a short explanation about what is written to each column of the file.
What columns are printed depend on what is switched on in your .edi file.

Best,
  Carsten


 I followed Spiwok's tutorial (http://web.vscht.cz/~spiwokv/mtdec/index.html) 
 and Langer's paper 
 (http://onlinelibrary.wiley.com/doi/10.1002/jcc.20473/full) . 
 
 Thanks, 
 
 
 
 
 
 --- 
 Biological Chemistry and Physics 
 Faculty of Pharmaceutical Sciences at Ribeirão Preto 
 University of São Paulo - Brazil 
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

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