Re: [gmx-users] regarding MSD

[Nidhi Katyal]

Hello

I have posted the query earlier but havent got any reply and so reposting
it again.

I have read few papers that determine transition temperature from the plot
of average MSD of hydrogen atoms of protein 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)?

Actually I am trying to reproduce the results of some published data.
Although I am getting the same transition temperature but the MSD values
are coming different (eg at a particular temperature if I average all the
MSD values, I am getting value of 15000 while reported value is 1.5 - both
values in same unit angstrom square)

Any help is highly appreciated.



On Thu, Aug 21, 2014 at 9:56 PM, Nidhi Katyal 
wrote:

> 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] Interteting flooding results

[Carsten Kutzner]

Hi,

On 21 Aug 2014, at 23:27, Ricardo O. S. Soares  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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Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
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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  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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--
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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
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Re: [gmx-users] too many lincs warnings

[Meenakshi Rajput]

Thanks..
On Aug 20, 2014 1:29 PM, "Meenakshi Rajput"  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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[gmx-users] Job Submission script for Multiple nodes GPUs calculation

[Xingcheng Lin]

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

Any suggestion about what I should do?

Thank you,

Arrow
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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  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 
> wrote:
>
> > On Wed, Aug 13, 2014 at 1:19 PM, Johnny Lu 
> 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.

[gmx-users] Interteting flooding results

[Ricardo O. S. Soares]

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? 
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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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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[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] 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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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  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 
> 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
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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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  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
> --
> Gromacs Users mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>
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[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] [gmx-developers] About dynamics loading balance

[Yunlong Liu]

Hi Roland,

I just compiled the latest gromacs-5.0 version released on Jun 29th. I 
will recompile it as you suggested by using those Flags. It seems like 
the high loading imbalance doesn't affect the performance as well, which 
is weird.


Thank you.
Yunlong
On 8/21/14, 2:13 PM, Roland Schulz wrote:

Hi,


On Thu, Aug 21, 2014 at 1:56 PM, Yunlong Liu > 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 mailto: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

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

[Roland Schulz]

Hi,


On Thu, Aug 21, 2014 at 1:56 PM, Yunlong Liu  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  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:
>> /home1/0300

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 
wrote:

> On Wed, Aug 13, 2014 at 1:19 PM, Johnny Lu  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.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] [gmx-developers] About dynamics loading balance

[Roland Schulz]

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  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 1020720 bytes for dest->a,
> dest->a=d5800030
> (called from file
> /home1/03002/yliu120/build/gromacs-5.0/src/gromacs/mdlib/domdec_top.c, line
> 1061)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> : Cannot allocate memory
> Error on rank 0, will try to stop all ranks
> Halting parallel program mdrun_mpi on CPU 0 out of 4
>
> gcq#274: "I Feel a Great Disturbance in the Force" (The Emperor Strikes
> Back)
>
> [cli_0]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
> [c442-702.stampede.tacc.utexas.edu:mpispawn_0][readline] Unexpected
> End-Of-File on file descriptor 6. MPI process died?
> [c442-702.stampede.tacc.utexas.edu:mpispawn_0][mtpmi_processops] Error
> while reading PMI socket. MPI process died?
> [c442-702.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process
> (rank: 0, pid: 112839) exited with status 255
> TACC: MPI job exited with code: 1
>
> TACC: Shutdown complete. Exiting.
>
> So I manually turned off the dynamic loading balance by -dlb no. The
> simulation goes through with the very high loading imbalance, like:
>
> DD  step 13 load imb.: force 51.3%
>
>Step   Time Lambda
>  14  280.00.0
>
>Energies (kJ/mol)
> U-BProper Dih.  Improper Dih.  CMAP Dih.  LJ-14
> 4.88709e+041.21990e+042.99128e+03   -1.46719e+031.98569e+04
>  Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> 2.54663e+054.05141e+05   -3.16020e+04   -3.75610e+062.24819e+04
>   PotentialKinetic En.   Total EnergyTemperature Pres. DC (bar)
>-3.02297e+066.15217e+05   -2.40775e+063.09312e+02   -2.17704e+02
>  Pressure (bar)   Constr. rmsd
>-3.39003e+013.10750e-05
>
> DD  step 14 load imb.: force 60.8%
>
>Step   Time Lambda
>  15  300.00.0
>
>Energies (kJ/mol)
> U-BProper Dih.  Improper Dih.  CMAP Dih.  LJ-14
> 4.96380e+041.21010e+042.99986e+03   -1.51918e+031.97542e+04
>  Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> 2.54305e+054.06024e+05   -3.15801e+04   -3.75534e+062.24001e+04
>   PotentialKinetic En.   Total EnergyTemperature Pres. DC (bar)
>-3.02121e+066.17009e+05   -2.40420e+063.10213e+02   -2.17403e+02
>  Pressure (bar)   Constr. rmsd
>-1.40623e+003.16495e-05
>
> I think this high loading imbalance will affect more than 20% of the
> performance but at least it will let the simulation on. Therefore, the
> problem I would like to report is that when running simulation with GPU-CPU
> hybrid with very few GPU, the dynamic loading balance will cause domain
> decomposition problems ( fail-to-allocate-memory ). I don't know whether
> there is any solution to this problem currently or anything could be
> improved?
>
> Yunlong
>
>
>
>
> --
>
> 
> Yunlong Liu, PhD Candidate
> Computational Biology and Biophysics
> Department of Biophysics and Biophysical Chemistry
> School of Medicine, The Johns Hopkins University
> Email: yliu...@jhmi.edu
> Address: 725 N Wolfe St, WBSB RM 601, 21205
> 
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-- 
Gromacs Users maili

Re: [gmx-users] Extending simulation problem.

[Mark Abraham]

On Thu, Aug 21, 2014 at 6:28 PM, Dawid das  wrote:

> Well in my *log file nothing about state or *cpi files is mentioned.
>

Sounds like perhaps your combination of circumstances (-append, no old
output files provided for appending, maybe not even a checkpoint file
provided) is leading to mdrun silently doing the only thing it can do,
which is start again from either the -s or -cpi state. Your description of "I
tried both state.cpt and prev_state.cpt and the beginning of new simulation
looks exactly the same" doesn't help fully - same as what? The start of the
first simulation, or the end of the first simulation?

There are some technical reasons why less output might be written when
doing mdrun -cpi -append, but your description does not make clear whether
they apply.

Acutally I have a question regarding state.cpi files. Does it contain names
> of *gro, *trr, etc. files if they are not standard?
>

Yes, even if not standard. You can see this with gmx dump -cp state.cpi


> 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?
>

You need to provide the files, however they are named, if you want to do
appending.


> And when I run another 5 ns should I run mdrun with those -c -o and -e
> options?


Yes, or use the -deffnm option to save yourself typing (and errors).


> If yes, should the names of files be the same as in the previous
> simulation?
>

Yes. Or use mdrun -noappend and do your concatenation later, old-school
style.

Mark


>
> 2014-08-20 18:18 GMT+01:00 Justin Lemkul :
>
> >
> >
> > 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 2>&1
> >>
> >> 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
> >
> > ==
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>
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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 :

>
>
> 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 2>&1
>>
>> 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
>
> ==
> --
> Gromacs Users mailing list
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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] 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  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
> --
> Gromacs Users mailing list
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> * Please search the archive at
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Re: [gmx-users] REMD tutorial

[Mark Abraham]

On Thu, Aug 21, 2014 at 8:01 AM, shahab shariati 
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+tutorials&oq=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] Several questions about log file.

[Mark Abraham]

On Thu, Aug 21, 2014 at 7:57 AM, Theodore Si  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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[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] 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"  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 
>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
>> from your computer and network.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>--
>Gromacs Users mailing list
>
>* Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>posting!
>
>* Can't post? Read http://

Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues

[Michael Carter]

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"  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 
>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
>> from your computer and network.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
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>
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>posting!
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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 
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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] Install errors

[Valentina Loconte]

Thanks!


2014-08-20 14:05 GMT+02:00 Mark Abraham :

> 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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-- 
Valentina Loconte, PhD student
Department of Biomedical Sciences
University of Padova
Viale G. Colombo 3
35131 Padova, Italy
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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  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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[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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