Re: Re: Re: [gmx-users] GPU-based workstation

[James Starlight]

On Nvidia benchmarks I've found suggestions of using of the two 6 cores CPU
for systems with the 2 GPU.

Assuming that I'll be using two 680 GTX cards with 256 bits and 4gb ram
(not a profesional nvidia cards like TESLA)
what CPU's could give me the best performance- 1 i7 of 8 cores
or 2 Xeons e5 with 6 cores ? Does it meaningful to use 2 separate CPU's
with several nodes each for the 2 GPU's ?

James

2013/5/26 lloyd riggs 

>
> You can also look at profilling on varied web sites, the high end Nvidia
> run only slightly better than the 2 year old ones, from an individual point
> not worth the money yet, but if you have the money? as I've been browsing.
>
> Also, the sim I did on the cluster was 180-190,000 atoms so the exact same
> performance the other person had.
>
> Stephan
>  *Gesendet:* Samstag, 25. Mai 2013 um 15:19 Uhr
> *Von:* "James Starlight" 
>
> *An:* "Discussion list for GROMACS users" 
> *Betreff:* Re: Aw: Re: [gmx-users] GPU-based workstation
> Richard,
>
> thanks for suggestion!
>
> Assuming that I'm using 2 high end GeForce's what performance be better
>
> 1) in case of one i7 (4 or 6 nodes ) ?
>
> 2) in case of 8 core Xeon like CPU Intel Xeon E5-2650 2.0 GHz / 8core
>
> What properties of MB should take into account primarily for such
> Xenon-based system. Does such MBs support multi-GPU ( I noticed that many
> such MBs lack for PCI)?
>
> James
>
> 2013/5/25 Broadbent, Richard 
>
> > I've been running on my Universities GPU nodes these are one E5-xeon
> > (6-cores 12 threads) and have 4 Nvidia 690gtx's. My system is 93 000
> atoms
> > of DMF under NVE. The performance has been a little disappointing
> > ~10ns/day. On my home system using a core i5-2500 and a nvidia 560ti I
> get
> > 5.4ns/day for the same system. On our HPC system using 32 nodes each
> with 2
> > quad-core xeon processors I get 30-40ns/day.
> >
> > I think that to achieve reasonable performance the system has to be
> > balanced between CPU's and GPU's probably getting 2 high end GPU's and a
> > top end xeon E5 or core i7 would be a good choice.
> >
> >
> > Richard
> >
> > From: lloyd riggs mailto:lloyd.ri...@gmx.ch>>
> > Reply-To: Discussion users  > gmx-users@gromacs.org>>
> > Date: Saturday, 25 May 2013 12:02
> > To: Discussion users mailto:gmx-users@gromacs.org
> >>
> > Subject: Aw: Re: [gmx-users] GPU-based workstation
> >
> > More RAM the better, and the best I have seen is 4 GPU work station. I
> > can use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is
> > really 3-4 GPU, except the tyan mentioned (there designed as blades so
> an 8
> > or 10 slot board really holds 8 or 10 GPU's). There's cooling problems
> > though with GPU's, as on a board there packed, so extra cooling things
> may
> > help not blow a GPU, but I would look for good ones (ask around), as its
> a
> > video game market and they go for looks even though its in casing? The
> > external RAM (not onboard GPU RAM) helps if you do a larger sim, but I
> dont
> > know performance wise, the onboard GPU, the more RAM the marrier...so
> yes,
> > normal work stations you can get 4 GPU's for a 300 US$ board, but then
> the
> > price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad
> > is also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on
> tests
> > software, not Gromacs, so would be nice to see performance...for a small
> > 100 atom molecule and 500 solvent, using just the CPU I get it to run
> 5-10
> > minutes real for 1 ns sim, but tried simple large 800 amino, 25,000
> > solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say
> > 50 ps eq's
> >
> > Stephan
> >
> > Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
> > Von: "James Starlight"  > jmsstarli...@gmail.com>>
> > An: "Discussion list for GROMACS users"  > gmx-users@gromacs.org>>
> > Betreff: Re: [gmx-users] GPU-based workstation
> > Dear Dr. Watkins!
> >
> > Thank you for the suggestions!
> >
> > In the local shops I've found only Core i7 with 6 cores (like Core
> > i7-39xx) and 4 cores. Should I obtain much better performance with 6
> cores
> > than with 4 cores in case of i7 cpu (assuming that I run simulation in
> > cpu+gpu mode )?
> >
> > Also you've mentioned about 4 PCeI MD. Does it means that modern
> > work-station could have 4 GPU's in one home-like desktop ? According to
> my
> > current task I suppose that 2 GPU's would be suitable for my simulations
> > (assuming that I use typical ASUS MB and 650 Watt power unit). Have
> > someone tried to use several GPU's on one workstation ? What attributes
> of
> > MB should be taken into account for best performance on such multi-gpu
> > station ?
> >
> > James
> >
> > 2013/5/25 lloyd riggs mailto:lloyd.ri...@gmx.ch>>
> >
> > > There's also these, but 1 chip runs 6K US, they can get performance up
> to
> > > 2.3 teraflops per chip though double percission...but have no clue
> about
> > > integration with GPU's...Intell also sells their chips on PCIe
> > cards...but
> > > get only

[gmx-users] Re: QM/MM simulations

[DavidPO]

I am sending you a . topol.tpr
  tpr file




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[gmx-users] Re: QM/MM simulations

[DavidPO]

I am sending you a .tpr file
topol.tpr   

David



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[gmx-users] FEP of ion binding protein

[Steven Neumann]

Dear Gmx Users,

I wish to compare binding free energy obtained from US which I have
sucsessfully conducted and the one obtained using FEP. Would you suggest
any tutorial?

Steven
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[gmx-users] (no subject)

[Ishwor Poudyal]

Dear all.I want to study Diffusion coefficient of carbonmonoxide in water...I 
get different values of force constant partial charge while searching for those 
constants. Can anyone help me providing the values of partial charge (of CO), 
force constant and lennard jones parameter used in the simulation 
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[gmx-users] Re: FEP of ion binding protein

[maggin]

Hi, Steven,

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html

and there is one paper"Good Practices in Free-Energy Calculations  J. Phys.
Chem. B, 2010, 114 (32), pp 10235–10253"

Hope this data could help you!

maggin



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[gmx-users] how to get the epsilon and sigma values of CO

[Ishwor Poudyal]

Dear all.I want to study simulation of  carbonmonoxide in water...I get 
different values of force constant partial charge while searching for those 
constants. Can anyone help me providing the values of partial charge (of CO), 
force constant and lennard jones parameter epsilon and sigma used in the 
simulation processThanks ----
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Re: [gmx-users] how to get the epsilon and sigma values of CO

[Dr. Vitaly Chaban]

if there are many values in the literature, what do you want?


On Mon, May 27, 2013 at 4:29 PM, Ishwor Poudyal wrote:

> Dear all.I want to study simulation of  carbonmonoxide in water...I get
> different values of force constant partial charge while searching for those
> constants. Can anyone help me providing the values of partial charge (of
> CO), force constant and lennard jones parameter epsilon and sigma used in
> the simulation processThanks --
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[gmx-users] Gromacs for Non biological systems

[Jeya vimalan]

Dear Collegues,
I was pointed to Gromacs to make it work
on the non biological systems.
My aim is to understand the interaction
of Hf precursors on Gamma Alumina surface.
But, i do not know yet if gromacs can efficiently handle this.
Can someone help me fiding some papers where GROMACS have been used for the
non biological system.
jeya
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[gmx-users] Using many index file in one command line

[Kieu Thu Nguyen]

Dear users,

Is there command for using many different index.ndx files in one command
line ? I used -n flag many times and gromacs report error.

Thankful for any help!
Thu
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Re: [gmx-users] Re: FEP of ion binding protein

[Justin Lemkul]

On 5/27/13 10:10 AM, maggin wrote:

Hi, Steven,

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html



Note that FEP (as requested in the original post) and BAR (used in the tutorial) 
are different methods for evaluating the free energy differences between states.


-Justin


and there is one paper"Good Practices in Free-Energy Calculations  J. Phys.
Chem. B, 2010, 114 (32), pp 10235–10253"

Hope this data could help you!

maggin



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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: QM/MM simulations

[Justin Lemkul]

On 5/27/13 7:17 AM, DavidPO wrote:

I am sending you a .tpr file
topol.tpr 



Thanks.  I can reproduce the problem.  I'll do a little digging and probably 
open a bug report.  Compilation proceeds without any issue, though it appears to 
result in a nonfunctional QM-enabled mdrun executable.  That definitely smells 
buggy to me.


-Justin

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Re: [gmx-users] Using many index file in one command line

[Terry]

Use make_ndx to put all your groups in one .ndx file. It's totally
unnecessary to use multiple .ndx file in one command.

Terry



On Tue, May 28, 2013 at 10:18 AM, Kieu Thu Nguyen wrote:

> Dear users,
>
> Is there command for using many different index.ndx files in one command
> line ? I used -n flag many times and gromacs report error.
>
> Thankful for any help!
> Thu
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Re: [gmx-users] Using many index file in one command line

[Justin Lemkul]

On 5/27/13 10:18 PM, Kieu Thu Nguyen wrote:

Dear users,

Is there command for using many different index.ndx files in one command
line ? I used -n flag many times and gromacs report error.



No Gromacs program accepts multiple index files simultaneously.  You must 
specify whatever groups you need in one index file.  The .ndx format is just 
plain text; you can even just concatenate index files with cat.


-Justin

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Re: [gmx-users] Using many index file in one command line

[Kieu Thu Nguyen]

Thank Terry and Justin so much ! I got it :-)


On Tue, May 28, 2013 at 9:20 AM, Justin Lemkul  wrote:

>
>
> On 5/27/13 10:18 PM, Kieu Thu Nguyen wrote:
>
>> Dear users,
>>
>> Is there command for using many different index.ndx files in one command
>> line ? I used -n flag many times and gromacs report error.
>>
>>
> No Gromacs program accepts multiple index files simultaneously.  You must
> specify whatever groups you need in one index file.  The .ndx format is
> just plain text; you can even just concatenate index files with cat.
>
> -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] Lennard Jones parameters

[Ishwor]

Dear all
I want to study the simulation of Carbonmonoxide in water. I have seen the
Lennard Jones parameters, force constant and partial charges of water in the
file spce.itp inherent in gromacs but couldnt get the parameters for CO .I
will be pleased if anyone provide me the LJ parameters (epsilon and sigma)
,partial charge of Carbon Monoxide.Due to some technical diffculties I have
got no access for the published papers.  Thanks 




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[gmx-users] Re: GPU-based workstation

[Ehud Schreiber]

I have nothing to contribute regarding the CPUs, but note that last week Nvidia 
introduced the GTX 780 GPU (a "Titan lite"), and this week it is expected to 
introduce the GTX 770 one (probably an "overclocked 680"). Therefore, 
disregarding possible price issues, it seems that the GTX 680 may not be the 
best option.



>Date: Mon, 27 May 2013 14:14:51 +0400

>From: James Starlight mailto:jmsstarli...@gmail.com>>

>Subject: Re: Re: Re: [gmx-users] GPU-based workstation

>To: Discussion list for GROMACS users 
>mailto:gmx-users@gromacs.org>>

>Message-ID:

> 
> mailto:CAALQopymnZm5r+3q4LK_ncM=vots3fvukbeky4k3pk27n2x...@mail.gmail.com>>

>Content-Type: text/plain; charset=ISO-8859-1

>

>On Nvidia benchmarks I've found suggestions of using of the two 6 cores CPU 
>for systems with the 2 GPU.

>

>Assuming that I'll be using two 680 GTX cards with 256 bits and 4gb ram (not a 
>profesional nvidia cards like TESLA) what CPU's >could give me the best 
>performance- 1 i7 of 8 cores or 2 Xeons e5 with 6 cores ? Does it meaningful 
>to use 2 separate CPU's with >several nodes each for the 2 GPU's ?

>

>James

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[gmx-users] choice of forcefield

[Revthi Sanker]

Dear all,
I am a beginner to performing simulations and my system consists of protein+ 
cholesteryl ester +phospholipid and drug. Papers involving lipids are in 
general united atom, while those involving drug-protein systems are all-atom 
mostly. Kindly suggest me which of these, all-atom or united atom should I be 
using for my system.

Thanks for your help in advance
Yours sincerely,
Revathi
M.S. Research Scholar
Indian Institute of Technology,Madras
India
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[gmx-users] ion mutation in FEP

[SEMRAN İPEK]

Dear Users,

I have been trying to carry out FEP calculations for a long time for
mutation of
Glutamine to Aspartic acid using gromacs 4.5.5. Unfortunately, some
questions and problems arises during calculations.
Here is the question of mine.With glutamine, the
protein charge is -12. To neutralize the system, I added 12 Na+ ions. When I
mutate GLN to ASP, the charge in state_B is -13. After I run the grompp
command, the result says that my State_B topology has -13 charge since I am
not including mutation of ion.
How can I mutate 1 particular ion to ensure the neutrality of the
state_B. How should I exactly modify my topology file to include counter
ions
for state B.
I am including the part of the mutation in topology file at the end of the
e-mail.
If you could help me, I really appreciate for you time and help.

 Residue 221 GLN rtp GLN ; q 0.0
2083 N 221 GLN N 894 -0.31 14.0067 ; qtot -4.31
2084 H 221 GLN H 894 0.31 1.008 ; qtot -4
2085 CH1 221 GLN CA 895 0 13.019 ; qtot -4
2086 CH2 221 GLN CB 895 0 14.027 ; qtot -4
2087 CH2 221 GLN CG 895 0 14.027 DUM 0 14.027 ; qtot -4
2088 C 221 GLN CD 896 0.29 12.011 C 0.27 12.011 ; qtot -3.71
2089 O 221 GLN OE1 896 -0.45 15.9994 OM -0.635 15.9994 ; qtot -4.16

2090 NT 221 GLN NE2 896 -0.72 14.0067 OM -0.635 15.9994 ; qtot -4.88
2091 H 221 GLN HE21 896 0.44 1.008 DUM 0 1.008 ; qtot -4.44
2092 H 221 GLN HE22 896 0.44 1.008 DUM 0 1.008 ; qtot -4
2093 C 221 GLN C 897 0.45 12.011 ; qtot -3.55
2094 O 221 GLN O 897 -0.45 15.9994 ; qtot -4
**


[ moleculetype ]
; Name nrexcl
NA+Mg 1

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 NA+ 20167 NA NA+ 1 1.0 22.9898 MG2+ 2.0 24.30 500


; Compound #mols
Protein_chain_C 1
FMT 1
SOL 19795
NA 12
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