Re: [gmx-users] >60% slowdown with GPU / verlet and sd integrator

[victor doss]

The paper looks good.  Do some more work and publish many


Sent from my iPhone

On 17-Jan-2013, at 8:18 PM, "James Starlight"  wrote:

Dear Gromacs Developers!

Using sd1 integrator I've obtain good performance with the core-5 +
GTX 670 ( 13ns\per day) for the system of 60k atoms. That results on
30% better than with the sd integrator.

Buit on my another work-station  which differs only by slower GPU ( GT
640). I've obtained some gpu\cpu mis-match.

Force evaluation time GPU/CPU: 6.835 ms/2.026 ms = 3.373( # on
the first station with GTX 670 I ve obtained GPU/CPU: ratio close to
1.

At both cases I'm using the same simulation parameters with 0,8
cutoffs (it's also important that in the second case I've calculated
another system consisted of 33k atoms by means of umbrella sampling
pulling)). Could you tell me how I could increase performance on my
second station ( to reduce gpucpu ratio) ?  I've attached log for that
simulation here http://www.sendspace.com/file/x0e3z8

James

2013/1/17 Szilárd Páll :
> Hi,
> 
> Just to note for the users who might read this: the report is valid, some
> non-thread-parallel code is the reason and we hope to have a fix for 4.6.0.
> 
> For updates, follow the issue #1211.
> 
> Cheers,
> 
> --
> Szilárd
> 
> 
> On Wed, Jan 16, 2013 at 4:45 PM, Berk Hess  wrote:
> 
>> 
>> The issue I'm referring to is about a factor of 2 in update and
>> constraints, but here it's much more.
>> I just found out that the SD update is not OpenMP threaded (and I even
>> noted in the code why this is).
>> I reopened the issue and will find a solution.
>> 
>> Cheers.
>> 
>> Berk
>> 
>> 
>>> Date: Wed, 16 Jan 2013 16:20:32 +0100
>>> Subject: Re: [gmx-users] >60% slowdown with GPU / verlet and sd
>> integrator
>>> From: mark.j.abra...@gmail.com
>>> To: gmx-users@gromacs.org
>>> 
>>> We should probably note this effect on the wiki somewhere?
>>> 
>>> Mark
>>> 
>>> On Wed, Jan 16, 2013 at 3:44 PM, Berk Hess  wrote:
>>> 
 
 Hi,
 
 Unfortunately this is not a bug, but a feature!
 We made the non-bondeds so fast on the GPU that integration and
 constraints take more time.
 The sd1 integrator is almost as fast as the md integrator, but slightly
 less accurate.
 In most cases that's a good solution.
 
 I closed the redmine issue:
 http://redmine.gromacs.org/issues/1121
 
 Cheers,
 
 Berk
 
 
> Date: Wed, 16 Jan 2013 17:26:18 +0300
> Subject: Re: [gmx-users] >60% slowdown with GPU / verlet and sd
 integrator
> From: jmsstarli...@gmail.com
> To: gmx-users@gromacs.org
> 
> Hi all!
> 
> I've also done some calculations with the SD integraator used as the
> thermostat ( without t_coupl ) with the system of 65k atoms I
>> obtained
> 10ns\day performance on gtc 670 and 4th core i5.
> I haventrun any simulations with MD integrator yet so It should test
>> it.
> 
> James
> 
> 2013/1/15 Szilárd Páll :
>> Hi Floris,
>> 
>> Great feedback, this needs to be looked into. Could you please
>> file a
 bug
>> report, preferably with a tpr (and/or all inputs) as well as log
>> files.
>> 
>> Thanks,
>> 
>> --
>> Szilárd
>> 
>> 
>> On Tue, Jan 15, 2013 at 3:50 AM, Floris Buelens <
 floris_buel...@yahoo.com>wrote:
>> 
>>> Hi,
>>> 
>>> 
>>> I'm seeing MD simulation running a lot slower with the sd
>> integrator
 than
>>> with md - ca. 10 vs. 30 ns/day for my 47000 atom system. I found
>> no
>>> documented indication that this should be the case.
>>> Timings and logs pasted in below - wall time seems to be
>> accumulating
 up
>>> in Update and Rest, adding up to >60% of total. The effect is
>> still
 there
>>> without GPU, ca. 40% slowdown when switching from group to Verlet
 with the
>>> SD integrator
>>> System: Xeon E5-1620, 1x GTX 680, gromacs
>>> 4.6-beta3-dev-20130107-e66851a-unknown, GCC 4.4.6 and 4.7.0
>>> 
>>> I didn't file a bug report yet as I don't have much variety of
>> testing
>>> conditions available right now, I hope someone else has a moment
>> to
 try to
>>> reproduce?
>>> 
>>> Timings:
>>> 
>>> cpu (ns/day)
>>> sd / verlet: 6
>>> sd / group: 10
>>> md / verlet: 9.2
>>> md / group: 11.4
>>> 
>>> gpu (ns/day)
>>> sd / verlet: 11
>>> md / verlet: 29.8
>>> 
>>> 
>>> 
>>> **MD integrator, GPU / verlet
>>> 
>>> M E G A - F L O P S A C C O U N T I N G
>>> 
>>> NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet
>> kernels
>>> RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
>>> W3=SPC/TIP3p W4=TIP4p (single or pairs)
>>> V&F=Potential and force V=Potential only F=Force only
>>> 
>>> Computing: M-Number M-Flops % Flops
>>> 

Re: [gmx-users] Re: meta-dynamics in gromacs-4.6

[James Starlight]

Dear Developers!

Today in the download section on gromacs web I've found 2 new verions
of gromacs ( 4.6 and 4.5.6) aviable for downloading. Does it final
releases and in what they differs?Have both of them  native GPU
support ?


James

2013/1/17 James Starlight :
> Thank you!
>
> It's a good news!
>
> James
>
> 2013/1/17 Carlo Camilloni :
>> Hi,
>>
>> yes I can confirm you that PLUMED will be available for gromacs-4.6!
>> We are currently testing it.
>>
>> Carlo
>>
>>> Message: 6
>>> Date: Wed, 16 Jan 2013 12:54:11 -0500
>>> From: Michael Shirts 
>>> Subject: Re: [gmx-users] meta-dynamics in gromacs-4.6
>>> To: Discussion list for GROMACS users 
>>> Message-ID:
>>>   
>>> Content-Type: text/plain; charset=ISO-8859-1
>>>
>>> I assume PLUMED will be implemented for Gromacs 4.6, as many PLUMED
>>> developers use Gromacs.  Perhaps any PLUMED lurkers on the list can
>>> speak up. . . .
>>>
>>> On Wed, Jan 16, 2013 at 9:20 AM, Mark Abraham  
>>> wrote:
 The GROMACS team has no plans for that. The usual problem here is that
 everybody would like every algorithm included, but that developers with
 time and experience are scarce :-) It's an open source project though, so
 anyone can do whatever they like. We're prepared to consider inclusions to
 the main project.

 Note that we're doing a major rework of the code base to C++ in the next
 year (or more), so people implementing new features may wish to consider
 that in their choice to write code :-)

 Mark

 On Tue, Jan 15, 2013 at 2:26 PM, James Starlight 
 wrote:

> Dear Gromacs developers!
>
>
> There is well-known plugin plumed which can be used for implementation
> of meta-dynamics simulation if Gromacs-4.5. I wounder to know if it
> possible to include some meta-dynamics options in the new gromacs
> release ( similar to inclusion of essential dynamics sampling in
> previous gromacs versions) ?
>
>
> Thanks for attention,
> James
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[gmx-users] concatenate of .edr files

[dina dusti]

Dear GROMACS Users,

I have simulations with 120 ps and the file names are md.*, then I expended 
the time of simulation to 240 ps, with file names next as are follow:

tpbconv -s md.tpr -extend 120 -o next.tpr
mdrun -v -deffnm next -s next.tpr -cpi md.cpt

I use from trjcat to concatenate md.trr and next.trr but I don't know that how 
should I concatenate the md.edr to next.edr!
May I ask you to help me, Please?
Best Regards
Dina
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Re: [gmx-users] concatenate of .edr files

[Justin Lemkul]

On 1/19/13 5:48 AM, dina dusti wrote:

Dear GROMACS Users,

I have simulations with 120 ps and the file names are md.*, then I expended 
the time of simulation to 240 ps, with file names next as are follow:

tpbconv -s md.tpr -extend 120 -o next.tpr
mdrun -v -deffnm next -s next.tpr -cpi md.cpt

I use from trjcat to concatenate md.trr and next.trr but I don't know that how 
should I concatenate the md.edr to next.edr!
May I ask you to help me, Please?


eneconv

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] au-protein separate minimization

[fatemeh ramezani]

Dr. Justin

I want to do energy minimization of AU and Protein in separate steps and in 
last emails you said a way for this, is freezing of them. Then I decide to 
freeze AU and minimize Protein and in next step vise versa. I'm wrong?


Fatemeh Ramezani
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Re: [gmx-users] au-protein separate minimization

[Justin Lemkul]

On 1/19/13 7:11 AM, fatemeh ramezani wrote:

Dr. Justin

I want to do energy minimization of AU and Protein in separate steps and in 
last emails you said a way for this, is freezing of them. Then I decide to 
freeze AU and minimize Protein and in next step vise versa. I'm wrong?



You can certainly do that if you have a justifiable reason to.  There's nothing 
wrong with that, I just don't understand the point.


-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: au-protein separate minimization

[Hamid Mosaddeghi]

I have questions about your work:

1-I see previous your posts , do you have equlibrium  structure of gold
nanoparticle?

2- about nanoparticle, gold atoms at surface have difference behaviour of
internal atom?? do you idea about it?

3- you include interation of "Au" only with "S" according to GulP force
filed is it correct? this work is good for surface not for paticle?

4- you can define new ffag.itp ffag.n2t ffag.rtp for include in your
topology,this method is easy. insert new atoms in oplss and define all
proper intraction is difficult.

if possible for you please send for me your input files (modified force
field file) that you need to use it . Maybe I can help to you. 

my email is: hamid5920...@yahoo.com

I done simulation of interation metal surface (Au-ag-ni-pb-pt-al-pd,..) with
protein by gromacs and namd, but I want do  simulation of metal nanoparticle
(full flexible) with protein with copling of two or three softwares. 

best regards

hamid mosaddeghi



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Re: [gmx-users] g_bundle: angle with x or y axis.

[rajat desikan]

Why don't you try rotating your simulation box using editconf (.gro) or
trjconv (.xtc)


On Sat, Jan 19, 2013 at 5:39 AM, Mortuza Munna  wrote:

> Dear gromacs user,
> I have found that g_bundle can measure the angle between a group from
> index file and z-axis with the option -z. Is it possible to measure the
> angle of that group from index file with y-axis/x-axis? Any suggestion will
> be appreciable.
>
> Regards,
> Mortuza
>
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-- 
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Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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[gmx-users] concatenate of .edr files

[dina dusti]

Dear Justin,

Thank you very much from your help.

Best Regards
Dina




- Original Message -
From: Justin Lemkul 
To: dina dusti ; Discussion list for GROMACS users 

Cc: 
Sent: Saturday, January 19, 2013 3:16 PM
Subject: Re: [gmx-users] concatenate of .edr files



On 1/19/13 5:48 AM, dina dusti wrote:
> Dear GROMACS Users,
>
> I have simulations with 120 ps and the file names are md.*, then I 
> expended the time of simulation to 240 ps, with file names next as are 
> follow:
>
> tpbconv -s md.tpr -extend 120 -o next.tpr
> mdrun -v -deffnm next -s next.tpr -cpi md.cpt
>
> I use from trjcat to concatenate md.trr and next.trr but I don't know that 
> how should I concatenate the md.edr to next.edr!
> May I ask you to help me, Please?

eneconv

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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[gmx-users] au-protein simulation, water constraint_algorithm

[fatemeh ramezani]

Dr. Justin

In GOLP paper is written: Water molecules were kept rigid with the SETTLE 
algorithm,
but in its commented md.mdp file is written

define  =     
;GOLP has been tested with lincs only
constraint =  none
constraint_algorithm   = lincs

according to manual, SETTLE can be selected in the topology, means that with 
the above settings in md.mdp file, should I add 

[  settles  ]
;  OW    funct  doh dhh
1 1 0.1 0.16333 

in .top file?
Are these settings correct?
If that is the constraint = none, constraint_algorithm = lincs applies?

many thanks

Fatemeh Ramezani
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Re: [gmx-users] au-protein simulation, water constraint_algorithm

[Justin Lemkul]

On 1/19/13 10:46 AM, fatemeh ramezani wrote:

Dr. Justin

In GOLP paper is written: Water molecules were kept rigid with the SETTLE 
algorithm,
but in its commented md.mdp file is written

define  =
;GOLP has been tested with lincs only
constraint =  none
constraint_algorithm   = lincs

according to manual, SETTLE can be selected in the topology, means that with 
the above settings in md.mdp file, should I add

[  settles  ]
;  OWfunct  doh dhh
1 1 0.1 0.16333

in .top file?
Are these settings correct?
If that is the constraint = none, constraint_algorithm = lincs applies?



The SETTLE algorithm is always used for water unless -DFLEXIBLE is defined in 
the .mdp file.  Note the #ifdef blocks in the topology for water.


-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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[gmx-users] another qm/mm interface (using ase)

[Markus Kaukonen]

Dear All,

I made a qm/mm implementation using gromacs as mm part.
Qm part can be in principle any qm method (now only FHI-aims implemented).
There can be more than one QM regions.

Documentation:
https://wiki.fysik.dtu.dk/ase/ase/calculators/ase_qmmm_manyqm.html#module-ase_qmmm_manyqm

terveisin, Markus


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Re: [gmx-users] g_bundle: angle with x or y axis.

[Justin Lemkul]

On 1/18/13 7:09 PM, Mortuza Munna wrote:

Dear gromacs user,
I have found that g_bundle can measure the angle between a group from
index file and z-axis with the option -z. Is it possible to measure the angle 
of that group from index file with y-axis/x-axis? Any suggestion will be 
appreciable.



You cannot do this directly with g_bundle without modifying the source code to 
implement such functionality.


One approach would be to:

1. Use trjconv -sep to split your trajectory into individual frames (.pdb or 
.gro)
2. Rotate each frame to realign what was previously x or y with the z-axis.
3. Concatenate the frames with trjcat into a new trajectory
4. Apply g_bundle -z

The above approach can easily be scripted.

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] inquiring for solving trjconv problems

[Mehdi Bagherpour]

hello everybody

I have simulated DNA using CHARMM force field for 50 ns with 2 ps snapshots
for each step.
when I wanted to convert .xtc trajectory files to .pdb using trjconv,  some
of the snapshots were collaborated.
I have used periodic boundary conditions in this simulations.
To convert, I used bellow command:

trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center

In collaborated .pdb files two strands of DNA separated from each other.
when I used bellow command instead of above command, this collaborated .pdb
file will be corrected,
but some of the other .pdb files will be ruined as same as

trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol

would you please help me to solve this technical problem?

I am looking forward hearing of you,

Mehdi Bagher Poor
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Re: [gmx-users] g_bundle: angle with x or y axis.

[Justin Lemkul]

On 1/19/13 4:57 PM, Mortuza Munna wrote:

Thank you Justin and Rajat. It is a very helpful information for me indeed. It
seems, I have to write an awk/sed/bash script to rotate each split frame, as I
will have at least 3000 frames after splitting. Moreover, I have 30 simulations
like this. However, is it possible to rotate all the frames together with any
command of Gromacs?


Yes, as I said, it can all be scripted.

1. Run trjconv -sep (names all files like frame1.gro, frame2.gro, etc)
2. For-loop through each file applying editconf -rotate
3. Concatenate

-Justin


Thanks once again.

*/Regards,/*
*/Mortuza
/*


*From:* Justin Lemkul 
*To:* Mortuza Munna ; Discussion list for GROMACS users

*Sent:* Saturday, January 19, 2013 9:57 AM
*Subject:* Re: [gmx-users] g_bundle: angle with x or y axis.



On 1/18/13 7:09 PM, Mortuza Munna wrote:
 > Dear gromacs user,
 > I have found that g_bundle can measure the angle between a group from
 > index file and z-axis with the option -z. Is it possible to measure the angle
of that group from index file with y-axis/x-axis? Any suggestion will be
appreciable.
 >

You cannot do this directly with g_bundle without modifying the source code to
implement such functionality.

One approach would be to:

1. Use trjconv -sep to split your trajectory into individual frames (.pdb or 
.gro)
2. Rotate each frame to realign what was previously x or y with the z-axis.
3. Concatenate the frames with trjcat into a new trajectory
4. Apply g_bundle -z

The above approach can easily be scripted.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin






--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] inquiring for solving trjconv problems

[Justin Lemkul]

On 1/19/13 5:21 PM, Mehdi Bagherpour wrote:

hello everybody

I have simulated DNA using CHARMM force field for 50 ns with 2 ps snapshots
for each step.
when I wanted to convert .xtc trajectory files to .pdb using trjconv,  some
of the snapshots were collaborated.
I have used periodic boundary conditions in this simulations.
To convert, I used bellow command:

trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center

In collaborated .pdb files two strands of DNA separated from each other.
when I used bellow command instead of above command, this collaborated .pdb
file will be corrected,
but some of the other .pdb files will be ruined as same as

trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol

would you please help me to solve this technical problem?



Use -center, perhaps in conjunction with some custom index group that will serve 
as an adequate central group for processing.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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