Aw: [gmx-users] GPU-based workstation

[lloyd riggs]

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 about 350 Gflops, and run 1K US$.

 

http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor

http://www.xilinx.com/

 

They can design them though to fit a PCIe slot and run about the same, but still need the board, ram etc...

 

Mostly just to dream about, they say you can order them with radiation shielding as well...so...

 

Stephan Watkins

 

Gesendet: Freitag, 24. Mai 2013 um 13:17 Uhr
Von: "James Starlight" 
An: "Discussion list for GROMACS users" 
Betreff: [gmx-users] GPU-based workstation

Dear Gromacs Users!


I'd like to build new workstation for performing simulation on GPU with
Gromacs 4.6 native cuda support.
Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video
and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system
with SD integrator)


Now I'd like to build multi-gpu wokstation.

My question - How much GPU would give me best performance on the typical
home-like workstation. What algorithm of Ncidia GPU integration should I
use (e.g SLI etc) ?


Thanks for help,


James
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Re: [gmx-users] grommp problem in gromacs 4.6.1

[Mark Abraham]

Looks like it. Please open an issue at gromacs.redmine.org and attach
enough files and instructions to reproduce the problem.

Thanks

Mark
On May 24, 2013 9:48 PM, "cyberjhon"  wrote:

> Hi guys
>
> I am trying to generate a .tpr file using grommp in gromacs 4.6.1.
> Unfortunately I am obtaining a very strange error:
> ---
> Program grompp, VERSION 4.6.1
> Source code file:
> /N/u/ortgrp/Quarry/src/gromacs-4.6.1/src/kernel/toppush.c,
> line: 1336
>
> Fatal error:
> Atomtype Zn2+ not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> The problem is that I do not have Zn2+ in my files. Neither in the .gro or
> in the .top
> I tried with a previous version 4.5.5 and it worked perfectly.
> I am using opls and it does not contain Zn2+, so that is more rare.
>
> I can not attach the .gro and .top files because the are like 300MB each.
>
> Can you tell me something? is this a bug?
>
> Thanks
>
> John Michael
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/grommp-problem-in-gromacs-4-6-1-tp5008531.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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Aw: Re: [gmx-users] the "-dist" flag of g_hbond tool

[lloyd riggs]

 

The hydrogen bonding energy would have/is usefull to myself.  An example, I use the .ndx as you did below for protein-protein interactions only.  I get around 25 and 28 for two different states.  The interesting part is the 25 is about 7 times the delG, however the hydrogen bonds move much less, and remain in contact longer across the trajectory.  A nice hydrogen bonding energy (real Vs. Calculated) would have added a nice graph to make a point.

 

Sincerely,

 

Stephan Watkins

 

Gesendet: Freitag, 24. Mai 2013 um 16:04 Uhr
Von: "Erik Marklund" 
An: "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] the "-dist" flag of g_hbond tool

It used to be. I didn't realise it was still in the code. We experimented a bit with having a continuous bond criterion instead of a binary measure. It didn't do for us what we hoped it would so it was abandoned. I know that some people are using Espiniozas empirical formula for bond energy, however, so that code may be resurrected at some point.

Erik

On 24 May 2013, at 15:12, CHEN Pan  wrote:

> Yes. I have looked at it already. I may need to spend time to understand
> it.
>
> By the way, in the source code, it seems some part are written for
> calculating hydrogen bonding energy, but I haven't see any "flag command"
> could give a output of "hydrogen bonding energy" file. Is it still under
> development?
>
>
> 2013/5/24 Erik Marklund 
>
>> Hm. That is peculiar. The source code has the answer of course. I can have
>> a look next week to see why that is.
>>
>> Erik
>>
>> On 24 May 2013, at 14:11, CHEN Pan  wrote:
>>
>>> Hi,
>>>
>>> I have 512 donors and 1024 acceptors.
>>>
>>> I have just tested "g_hbond" with my standard crystal structure, which I
>>> should get 512 hydrogen bonds. And the output "hbnum.xvg" does show 512
>>> hydrogen bonds, which is correct. But the "hbdist.xvg" file still shows
>>> that the summation of population is 200.
>>>
>>>
>>> 2013/5/24 Erik Marklund 
>>>
 Hi,

 See below

 On 24 May 2013, at 11:45, CHEN Pan  wrote:

> Dear Gromacs users,
>
> I am confused about the g_hbond tools.
>
> 1) When I use "-dist" to get the distribution of hydrogen bonding
 distance,
> I found that the summation of the population is always 200 (the
>> y-column
> below). I am not sure if it's was done with normalization or not, if
>> yes,
> the summation should be one, if no, then the summation should equals to
 the
> total number of the hydrogen bonds, but here the "hbnum.xvg" shows me I
> have 440 hydrogen bonds. Why here is always 200, not matter what types
>> of
> hydrogen bonds.

 How many donors do you have, and how many acceptors?

>
> 2) In my system, there are several different types of hydrogen bonds,
 such
> as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen
> bonds. Is there any "smart" way to separately calculate those hydrogen
> bonds? By using the "index.ndx" file, I could separate the intra-chain
> hydrogen bonds, then I can get the inter-chain ones using the total one
> minus the intra-chain one. It may be possible to do the same for the
> intra-sheet and the inter-sheet. However, this strategy seems
>> "complex".
> Did anybody have experience or ideas for this problem?
>
> Pan
>
> # This file was created Fri May 24 11:06:01 2013
> # by the following command:
> # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s
> /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b
>> 11000
 -e
> 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g
> #
> # g_hbond is part of G R O M A C S:
> #
> # Gromacs Runs One Microsecond At Cannonball Speeds
> #
> @ title "Hydrogen Bond Distribution"
> @ xaxis label "Hydrogen - Acceptor Distance (nm)"
> @ yaxis label ""
> @TYPE xy
> 0.0025 0
> 0.0075 0
> 0.0125 0
> 0.0175 0
> 0.0225 0
> 0.0275 0
> 0.0325 0
> 0.0375 0
> 0.0425 0
> 0.0475 0
> 0.0525 0
> 0.0575 0
> 0.0625 0
> 0.0675 0
> 0.0725 0
> 0.0775 0
> 0.0825 0
> 0.0875 0
> 0.0925 0
> 0.0975 0
> 0.1025 0
> 0.1075 0
> 0.1125 0
> 0.1175 0
> 0.1225 0
> 0.1275 0
> 0.1325 0
> 0.1375 0
> 0.1425 0
> 0.1475 0
> 0.1525 0
> 0.1575 0
> 0.1625 0
> 0.1675 0
> 0.1725 0
> 0.1775 0
> 0.1825 0
> 0.1875 0
> 0.1925 0
> 0.1975 0
> 0.2025 0
> 0.2075 0
> 0.2125 0
> 0.2175 0
> 0.2225 0
> 0.2275 0
> 0.2325 0.00538632
> 0.2375 0.125501
> 0.2425 1.23562
> 0.2475 6.08295
> 0.2525 16.4279
> 0.2575 28.6597
> 0.2625 36.0576
> 0.2675 35.154
> 0.2725 28.1539
> 0.2775 19.8073
> 0.2825 12.4602
> 0.2875 7.23832
> 0.2925 4.06577
> 0.2975 2.15794
> 0.3025 1.14423
> 0.3075 0.588366
> 0.3125 0.310611
> 0.3175

Aw: [gmx-users] GPU-based workstation

[lloyd riggs]

Dear Dr. Starlight,

 

Dont know the answere to all, but funny I was looking at performance on varied others web sites.  I use a core i7 970, but it seems their newest chip is almost the same as the i7 in performance (thier newer chips dont scale past 12 cores for some internal chip based design, they put out a 60 core chip for 1K and it doesnt even reach 1 terflop), and the newer GPU's suffer from board IO limits due the PCIe being maxed out.

 

As far as boards, home PC (im in Switzerland so have been mind distroyed as far as prices), there's a 4 CPU 10 GPU tyan board for 4K US (if you dig enough maybe 3,500) which with ram, chips and a single Nvidia would run up to 5-6 K US$.  The i7 970's can be baught for 30-50 US$ a pop now if you look becuase intel overshot its abilities and gave off the rights to several bulk manufacturers (all LG 1366 socket chips even i5's) as they add more pins (2100 or something), but you have to spend a day or two on the internet looking through sellers abroad.  The Nvida's are the pricy thing, however from what I have read, you dont get much more from their latest as well as mentioned, so 2 more years waiting, or something like I mentioned with a 2 year old Nvidia or two, would be the best especially for research purposes.  Otherwise a single 300 US board with 4 usable PCIe's (ASUS arnt bad), ram, 1 i7 970, and 1 Nvida from 2 years back gives you around 1.3 terflops, with their lates 1.4-1.5 teraflops (integrated use of chip alone).  The i7 I have I have got around 350 Gflops for some things with 8 threads.  I use radeons though, although this requires user programming, and if you use ther FFT libraries, you have to sign your first child over and loose any freeware redistribution rights in any way, otherwise their supposedly supposed to have all the same CUDA like libraries by the end of the summer (Portlandgroup , openCL), but I heard the same for 2 years now.

 

Sincerely,

 

Stephan Watkins

 

Gesendet: Freitag, 24. Mai 2013 um 13:17 Uhr
Von: "James Starlight" 
An: "Discussion list for GROMACS users" 
Betreff: [gmx-users] GPU-based workstation

Dear Gromacs Users!


I'd like to build new workstation for performing simulation on GPU with
Gromacs 4.6 native cuda support.
Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video
and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system
with SD integrator)


Now I'd like to build multi-gpu wokstation.

My question - How much GPU would give me best performance on the typical
home-like workstation. What algorithm of Ncidia GPU integration should I
use (e.g SLI etc) ?


Thanks for help,


James
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Re: [gmx-users] On pressure controlling

[Justin Lemkul]

On 5/24/13 3:49 PM, Bao Kai wrote:

Dear all,

I am wondering if I can make the box only scale in one single direction,
such as the z direction when controlling the pressure so that I can fix the
area of the box in xy plane.

I just want to fix the area of the interface during the NPT simulation.



Set the compressibility to zero in whichever directions you want to fix, 
applying semiisotropic or anisotropic pressure coupling as needed.


-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] On pressure controlling

[Bao Kai]

Dear all,

I am wondering if I can make the box only scale in one single direction,
such as the z direction when controlling the pressure so that I can fix the
area of the box in xy plane.

I just want to fix the area of the interface during the NPT simulation.

Thanks a lot.

Best,
Kai
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[gmx-users] grommp problem in gromacs 4.6.1

[cyberjhon]

Hi guys

I am trying to generate a .tpr file using grommp in gromacs 4.6.1.
Unfortunately I am obtaining a very strange error:
---
Program grompp, VERSION 4.6.1
Source code file: /N/u/ortgrp/Quarry/src/gromacs-4.6.1/src/kernel/toppush.c,
line: 1336

Fatal error:
Atomtype Zn2+ not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

The problem is that I do not have Zn2+ in my files. Neither in the .gro or
in the .top 
I tried with a previous version 4.5.5 and it worked perfectly. 
I am using opls and it does not contain Zn2+, so that is more rare.

I can not attach the .gro and .top files because the are like 300MB each.

Can you tell me something? is this a bug?

Thanks 

John Michael




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[gmx-users] Re: Have your ever got a real NVE simulation (good energy conservation) in gromacs?

[cyberjhon]

Hi Guys

Thanks for your reply

1.  Ok guys I will use the following

Double precision gromacs

dt=1fs
pbc  = xyz

nstlist  = 5
rlist= 1.7
rlist_long   = 2.0

coulombtype  = PME-Switch
rcoulomb_switch   = 1.2
rcoulomb= 1.4

fourierspacing   = 0.12
pme_order= 6
ewald_rtol   = 1e-5
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = yes

vdw-type = Shift
rvdw-switch= 0
rvdw= 1.7

tcoupl   = no
pcoupl   = no

constraints  = h-bonds 
constraint-algorithm = Lincs
lincs-order  = 4
lincs-warnangle  = 30

2. Any other suggestion ??

Thanks

John Michael 





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Re: [gmx-users] the "-dist" flag of g_hbond tool

[Erik Marklund]

It used to be. I didn't realise it was still in the code. We experimented a bit 
with having a continuous bond criterion instead of a binary measure. It didn't 
do for us what we hoped it would so it was abandoned. I know that some people 
are using Espiniozas empirical formula for bond energy, however, so that code 
may be resurrected at some point.

Erik

On 24 May 2013, at 15:12, CHEN Pan  wrote:

> Yes. I have looked at it already. I may need to spend time to understand
> it.
> 
> By the way, in the source code, it seems some part are written for
> calculating hydrogen bonding energy, but I haven't see any "flag command"
> could give a output of "hydrogen bonding energy" file. Is it still under
> development?
> 
> 
> 2013/5/24 Erik Marklund 
> 
>> Hm. That is peculiar. The source code has the answer of course. I can have
>> a look next week to see why that is.
>> 
>> Erik
>> 
>> On 24 May 2013, at 14:11, CHEN Pan  wrote:
>> 
>>> Hi,
>>> 
>>> I have 512 donors and 1024 acceptors.
>>> 
>>> I have just tested "g_hbond" with my standard crystal structure, which I
>>> should get 512 hydrogen bonds. And the output "hbnum.xvg" does show 512
>>> hydrogen bonds, which is correct. But the "hbdist.xvg" file still shows
>>> that the summation of population is 200.
>>> 
>>> 
>>> 2013/5/24 Erik Marklund 
>>> 
 Hi,
 
 See below
 
 On 24 May 2013, at 11:45, CHEN Pan  wrote:
 
> Dear Gromacs users,
> 
> I am confused about the g_hbond tools.
> 
> 1) When I use "-dist" to get the distribution of hydrogen bonding
 distance,
> I found that the summation of the population is always 200 (the
>> y-column
> below). I am not sure if it's was done with normalization or not, if
>> yes,
> the summation should be one, if no, then the summation should equals to
 the
> total number of the hydrogen bonds, but here the "hbnum.xvg" shows me I
> have 440 hydrogen bonds. Why here is always 200, not matter what types
>> of
> hydrogen bonds.
 
 How many donors do you have, and how many acceptors?
 
> 
> 2) In my system, there are several different types of hydrogen bonds,
 such
> as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen
> bonds. Is there any "smart" way to separately calculate those hydrogen
> bonds? By using the "index.ndx" file, I could separate the intra-chain
> hydrogen bonds, then I can get the inter-chain ones using the total one
> minus the intra-chain one. It may be possible to do the same for the
> intra-sheet and the inter-sheet. However, this strategy seems
>> "complex".
> Did anybody have experience or ideas for this problem?
> 
> Pan
> 
> # This file was created Fri May 24 11:06:01 2013
> # by the following command:
> # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s
> /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b
>> 11000
 -e
> 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g
> #
> # g_hbond is part of G R O M A C S:
> #
> # Gromacs Runs One Microsecond At Cannonball Speeds
> #
> @title "Hydrogen Bond Distribution"
> @xaxis  label "Hydrogen - Acceptor Distance (nm)"
> @yaxis  label ""
> @TYPE xy
>  0.0025  0
>  0.0075  0
>  0.0125  0
>  0.0175  0
>  0.0225  0
>  0.0275  0
>  0.0325  0
>  0.0375  0
>  0.0425  0
>  0.0475  0
>  0.0525  0
>  0.0575  0
>  0.0625  0
>  0.0675  0
>  0.0725  0
>  0.0775  0
>  0.0825  0
>  0.0875  0
>  0.0925  0
>  0.0975  0
>  0.1025  0
>  0.1075  0
>  0.1125  0
>  0.1175  0
>  0.1225  0
>  0.1275  0
>  0.1325  0
>  0.1375  0
>  0.1425  0
>  0.1475  0
>  0.1525  0
>  0.1575  0
>  0.1625  0
>  0.1675  0
>  0.1725  0
>  0.1775  0
>  0.1825  0
>  0.1875  0
>  0.1925  0
>  0.1975  0
>  0.2025  0
>  0.2075  0
>  0.2125  0
>  0.2175  0
>  0.2225  0
>  0.2275  0
>  0.2325 0.00538632
>  0.2375   0.125501
>  0.24251.23562
>  0.24756.08295
>  0.252516.4279
>  0.257528.6597
>  0.262536.0576
>  0.2675 35.154
>  0.272528.1539
>  0.277519.8073
>  0.282512.4602
>  0.28757.23832
>  0.29254.06577
>  0.29752.15794
>  0.30251.14423
>  0.3075   0.588366
>  0.3125   0.310611
>  0.3175   0.163206
>  0.3225  0.0772039
>  0.3275  0.0411156
>  0.3325  0.0210066
>  0.337

Re: [gmx-users] the "-dist" flag of g_hbond tool

[CHEN Pan]

Yes. I have looked at it already. I may need to spend time to understand
it.

By the way, in the source code, it seems some part are written for
calculating hydrogen bonding energy, but I haven't see any "flag command"
could give a output of "hydrogen bonding energy" file. Is it still under
development?


2013/5/24 Erik Marklund 

> Hm. That is peculiar. The source code has the answer of course. I can have
> a look next week to see why that is.
>
> Erik
>
> On 24 May 2013, at 14:11, CHEN Pan  wrote:
>
> > Hi,
> >
> > I have 512 donors and 1024 acceptors.
> >
> > I have just tested "g_hbond" with my standard crystal structure, which I
> > should get 512 hydrogen bonds. And the output "hbnum.xvg" does show 512
> > hydrogen bonds, which is correct. But the "hbdist.xvg" file still shows
> > that the summation of population is 200.
> >
> >
> > 2013/5/24 Erik Marklund 
> >
> >> Hi,
> >>
> >> See below
> >>
> >> On 24 May 2013, at 11:45, CHEN Pan  wrote:
> >>
> >>> Dear Gromacs users,
> >>>
> >>> I am confused about the g_hbond tools.
> >>>
> >>> 1) When I use "-dist" to get the distribution of hydrogen bonding
> >> distance,
> >>> I found that the summation of the population is always 200 (the
> y-column
> >>> below). I am not sure if it's was done with normalization or not, if
> yes,
> >>> the summation should be one, if no, then the summation should equals to
> >> the
> >>> total number of the hydrogen bonds, but here the "hbnum.xvg" shows me I
> >>> have 440 hydrogen bonds. Why here is always 200, not matter what types
> of
> >>> hydrogen bonds.
> >>
> >> How many donors do you have, and how many acceptors?
> >>
> >>>
> >>> 2) In my system, there are several different types of hydrogen bonds,
> >> such
> >>> as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen
> >>> bonds. Is there any "smart" way to separately calculate those hydrogen
> >>> bonds? By using the "index.ndx" file, I could separate the intra-chain
> >>> hydrogen bonds, then I can get the inter-chain ones using the total one
> >>> minus the intra-chain one. It may be possible to do the same for the
> >>> intra-sheet and the inter-sheet. However, this strategy seems
> "complex".
> >>> Did anybody have experience or ideas for this problem?
> >>>
> >>> Pan
> >>>
> >>> # This file was created Fri May 24 11:06:01 2013
> >>> # by the following command:
> >>> # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s
> >>> /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b
> 11000
> >> -e
> >>> 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g
> >>> #
> >>> # g_hbond is part of G R O M A C S:
> >>> #
> >>> # Gromacs Runs One Microsecond At Cannonball Speeds
> >>> #
> >>> @title "Hydrogen Bond Distribution"
> >>> @xaxis  label "Hydrogen - Acceptor Distance (nm)"
> >>> @yaxis  label ""
> >>> @TYPE xy
> >>>   0.0025  0
> >>>   0.0075  0
> >>>   0.0125  0
> >>>   0.0175  0
> >>>   0.0225  0
> >>>   0.0275  0
> >>>   0.0325  0
> >>>   0.0375  0
> >>>   0.0425  0
> >>>   0.0475  0
> >>>   0.0525  0
> >>>   0.0575  0
> >>>   0.0625  0
> >>>   0.0675  0
> >>>   0.0725  0
> >>>   0.0775  0
> >>>   0.0825  0
> >>>   0.0875  0
> >>>   0.0925  0
> >>>   0.0975  0
> >>>   0.1025  0
> >>>   0.1075  0
> >>>   0.1125  0
> >>>   0.1175  0
> >>>   0.1225  0
> >>>   0.1275  0
> >>>   0.1325  0
> >>>   0.1375  0
> >>>   0.1425  0
> >>>   0.1475  0
> >>>   0.1525  0
> >>>   0.1575  0
> >>>   0.1625  0
> >>>   0.1675  0
> >>>   0.1725  0
> >>>   0.1775  0
> >>>   0.1825  0
> >>>   0.1875  0
> >>>   0.1925  0
> >>>   0.1975  0
> >>>   0.2025  0
> >>>   0.2075  0
> >>>   0.2125  0
> >>>   0.2175  0
> >>>   0.2225  0
> >>>   0.2275  0
> >>>   0.2325 0.00538632
> >>>   0.2375   0.125501
> >>>   0.24251.23562
> >>>   0.24756.08295
> >>>   0.252516.4279
> >>>   0.257528.6597
> >>>   0.262536.0576
> >>>   0.2675 35.154
> >>>   0.272528.1539
> >>>   0.277519.8073
> >>>   0.282512.4602
> >>>   0.28757.23832
> >>>   0.29254.06577
> >>>   0.29752.15794
> >>>   0.30251.14423
> >>>   0.3075   0.588366
> >>>   0.3125   0.310611
> >>>   0.3175   0.163206
> >>>   0.3225  0.0772039
> >>>   0.3275  0.0411156
> >>>   0.3325  0.0210066
> >>>   0.3375  0.0113113
> >>>   0.3425 0.00574541
> >>>   0.3475 0.00502723
> >>> --
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>> * Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or

Re: [gmx-users] the "-dist" flag of g_hbond tool

[Erik Marklund]

Hm. That is peculiar. The source code has the answer of course. I can have a 
look next week to see why that is.

Erik

On 24 May 2013, at 14:11, CHEN Pan  wrote:

> Hi,
> 
> I have 512 donors and 1024 acceptors.
> 
> I have just tested "g_hbond" with my standard crystal structure, which I
> should get 512 hydrogen bonds. And the output "hbnum.xvg" does show 512
> hydrogen bonds, which is correct. But the "hbdist.xvg" file still shows
> that the summation of population is 200.
> 
> 
> 2013/5/24 Erik Marklund 
> 
>> Hi,
>> 
>> See below
>> 
>> On 24 May 2013, at 11:45, CHEN Pan  wrote:
>> 
>>> Dear Gromacs users,
>>> 
>>> I am confused about the g_hbond tools.
>>> 
>>> 1) When I use "-dist" to get the distribution of hydrogen bonding
>> distance,
>>> I found that the summation of the population is always 200 (the y-column
>>> below). I am not sure if it's was done with normalization or not, if yes,
>>> the summation should be one, if no, then the summation should equals to
>> the
>>> total number of the hydrogen bonds, but here the "hbnum.xvg" shows me I
>>> have 440 hydrogen bonds. Why here is always 200, not matter what types of
>>> hydrogen bonds.
>> 
>> How many donors do you have, and how many acceptors?
>> 
>>> 
>>> 2) In my system, there are several different types of hydrogen bonds,
>> such
>>> as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen
>>> bonds. Is there any "smart" way to separately calculate those hydrogen
>>> bonds? By using the "index.ndx" file, I could separate the intra-chain
>>> hydrogen bonds, then I can get the inter-chain ones using the total one
>>> minus the intra-chain one. It may be possible to do the same for the
>>> intra-sheet and the inter-sheet. However, this strategy seems "complex".
>>> Did anybody have experience or ideas for this problem?
>>> 
>>> Pan
>>> 
>>> # This file was created Fri May 24 11:06:01 2013
>>> # by the following command:
>>> # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s
>>> /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b 11000
>> -e
>>> 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g
>>> #
>>> # g_hbond is part of G R O M A C S:
>>> #
>>> # Gromacs Runs One Microsecond At Cannonball Speeds
>>> #
>>> @title "Hydrogen Bond Distribution"
>>> @xaxis  label "Hydrogen - Acceptor Distance (nm)"
>>> @yaxis  label ""
>>> @TYPE xy
>>>   0.0025  0
>>>   0.0075  0
>>>   0.0125  0
>>>   0.0175  0
>>>   0.0225  0
>>>   0.0275  0
>>>   0.0325  0
>>>   0.0375  0
>>>   0.0425  0
>>>   0.0475  0
>>>   0.0525  0
>>>   0.0575  0
>>>   0.0625  0
>>>   0.0675  0
>>>   0.0725  0
>>>   0.0775  0
>>>   0.0825  0
>>>   0.0875  0
>>>   0.0925  0
>>>   0.0975  0
>>>   0.1025  0
>>>   0.1075  0
>>>   0.1125  0
>>>   0.1175  0
>>>   0.1225  0
>>>   0.1275  0
>>>   0.1325  0
>>>   0.1375  0
>>>   0.1425  0
>>>   0.1475  0
>>>   0.1525  0
>>>   0.1575  0
>>>   0.1625  0
>>>   0.1675  0
>>>   0.1725  0
>>>   0.1775  0
>>>   0.1825  0
>>>   0.1875  0
>>>   0.1925  0
>>>   0.1975  0
>>>   0.2025  0
>>>   0.2075  0
>>>   0.2125  0
>>>   0.2175  0
>>>   0.2225  0
>>>   0.2275  0
>>>   0.2325 0.00538632
>>>   0.2375   0.125501
>>>   0.24251.23562
>>>   0.24756.08295
>>>   0.252516.4279
>>>   0.257528.6597
>>>   0.262536.0576
>>>   0.2675 35.154
>>>   0.272528.1539
>>>   0.277519.8073
>>>   0.282512.4602
>>>   0.28757.23832
>>>   0.29254.06577
>>>   0.29752.15794
>>>   0.30251.14423
>>>   0.3075   0.588366
>>>   0.3125   0.310611
>>>   0.3175   0.163206
>>>   0.3225  0.0772039
>>>   0.3275  0.0411156
>>>   0.3325  0.0210066
>>>   0.3375  0.0113113
>>>   0.3425 0.00574541
>>>   0.3475 0.00502723
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
> 
> 
> 
> -- 
> Pan Chen
> CERMAV-CNRS
> BP 53
> 38041 Grenoble Cedex 9
> tel. +33 

[gmx-users] Re: GPU-based workstation

[James Starlight]

In particular I'd like to more carefully choose gpu card (and number of
cards) as well as CPU


1) In case of GPU I have to possible options
2 x GeForce 680 (256 bit, 4gb ram ) or 1 x  Geforce 690 (320 bit, 6 gb ram).
>From what option the best performance should be expected ? What GPU's
parameters would be most crucial for simulations ?

2) In case of CPU I'd like to use Core i7 (4 cores). Should the performance
with that CPU be better than with Core I5 ( also 4 cores) ?

3) Any other setups ? (e.g based on the server-like hardware Xeon CPU )
Could also someone provide me with some bechmark tests of new Gromacs 4.6
with different hardware setups ?

Thanks for help

James

2013/5/24 James Starlight 

> Dear Gromacs Users!
>
>
> I'd like to build new workstation for performing simulation on GPU with
> Gromacs 4.6 native cuda support.
> Recently I've used such setup with  Core i5 cpu and nvidia 670 GTX video
> and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system
> with SD integrator)
>
>
> Now I'd like to build multi-gpu wokstation.
>
> My question - How much GPU would give me best performance on the typical
> home-like workstation. What algorithm of Ncidia GPU integration should I
> use (e.g SLI etc) ?
>
>
> Thanks for help,
>
>
> James
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] the "-dist" flag of g_hbond tool

[CHEN Pan]

Hi,

I have 512 donors and 1024 acceptors.

I have just tested "g_hbond" with my standard crystal structure, which I
should get 512 hydrogen bonds. And the output "hbnum.xvg" does show 512
hydrogen bonds, which is correct. But the "hbdist.xvg" file still shows
that the summation of population is 200.


2013/5/24 Erik Marklund 

> Hi,
>
> See below
>
> On 24 May 2013, at 11:45, CHEN Pan  wrote:
>
> > Dear Gromacs users,
> >
> > I am confused about the g_hbond tools.
> >
> > 1) When I use "-dist" to get the distribution of hydrogen bonding
> distance,
> > I found that the summation of the population is always 200 (the y-column
> > below). I am not sure if it's was done with normalization or not, if yes,
> > the summation should be one, if no, then the summation should equals to
> the
> > total number of the hydrogen bonds, but here the "hbnum.xvg" shows me I
> > have 440 hydrogen bonds. Why here is always 200, not matter what types of
> > hydrogen bonds.
>
> How many donors do you have, and how many acceptors?
>
> >
> > 2) In my system, there are several different types of hydrogen bonds,
> such
> > as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen
> > bonds. Is there any "smart" way to separately calculate those hydrogen
> > bonds? By using the "index.ndx" file, I could separate the intra-chain
> > hydrogen bonds, then I can get the inter-chain ones using the total one
> > minus the intra-chain one. It may be possible to do the same for the
> > intra-sheet and the inter-sheet. However, this strategy seems "complex".
> > Did anybody have experience or ideas for this problem?
> >
> > Pan
> >
> > # This file was created Fri May 24 11:06:01 2013
> > # by the following command:
> > # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s
> > /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b 11000
> -e
> > 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g
> > #
> > # g_hbond is part of G R O M A C S:
> > #
> > # Gromacs Runs One Microsecond At Cannonball Speeds
> > #
> > @title "Hydrogen Bond Distribution"
> > @xaxis  label "Hydrogen - Acceptor Distance (nm)"
> > @yaxis  label ""
> > @TYPE xy
> >0.0025  0
> >0.0075  0
> >0.0125  0
> >0.0175  0
> >0.0225  0
> >0.0275  0
> >0.0325  0
> >0.0375  0
> >0.0425  0
> >0.0475  0
> >0.0525  0
> >0.0575  0
> >0.0625  0
> >0.0675  0
> >0.0725  0
> >0.0775  0
> >0.0825  0
> >0.0875  0
> >0.0925  0
> >0.0975  0
> >0.1025  0
> >0.1075  0
> >0.1125  0
> >0.1175  0
> >0.1225  0
> >0.1275  0
> >0.1325  0
> >0.1375  0
> >0.1425  0
> >0.1475  0
> >0.1525  0
> >0.1575  0
> >0.1625  0
> >0.1675  0
> >0.1725  0
> >0.1775  0
> >0.1825  0
> >0.1875  0
> >0.1925  0
> >0.1975  0
> >0.2025  0
> >0.2075  0
> >0.2125  0
> >0.2175  0
> >0.2225  0
> >0.2275  0
> >0.2325 0.00538632
> >0.2375   0.125501
> >0.24251.23562
> >0.24756.08295
> >0.252516.4279
> >0.257528.6597
> >0.262536.0576
> >0.2675 35.154
> >0.272528.1539
> >0.277519.8073
> >0.282512.4602
> >0.28757.23832
> >0.29254.06577
> >0.29752.15794
> >0.30251.14423
> >0.3075   0.588366
> >0.3125   0.310611
> >0.3175   0.163206
> >0.3225  0.0772039
> >0.3275  0.0411156
> >0.3325  0.0210066
> >0.3375  0.0113113
> >0.3425 0.00574541
> >0.3475 0.00502723
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Pan Chen
CERMAV-CNRS
BP 53
38041 Grenoble Cedex 9
tel. +33 (0)4 76 03 76 12
fax. +33 (0)4 76 54 72 03
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archi

Re: [gmx-users] Re: REMD analysis

[bharat gupta]

Dear Sir,

Thank you for the advice.  I have not understood the things properly,
especially the convergence of REMD. I got two relevant papers : 1. Convergence
of replica exchange molecular dynamics
2. Convergence and sampling efficiency in replica exchange simulations of
peptide folding in explicit solvent. If you can provide better reference
then this ...


Thank you francesco for the option. Indeed I was missing a a very imp.
option while plotting the data.


On Fri, May 24, 2013 at 7:40 PM, francesco oteri
wrote:

> Hi to everybody,
> Bharat, maybe i didn't follow exactly the wole tale, but is it possible you
> are running xmgrace without the -nxy option?
> You are probably visualizing the data related the 1st replica several
> times!
>
> Francesco
>
>
> 2013/5/24 Mark Abraham 
>
> > On Fri, May 24, 2013 at 10:44 AM, bharat gupta  > >wrote:
> >
> > > Dear Sir,
> > >
> > > Thank you for your detailed response to my query. I understood the
> > concept
> > > of ordered arrangement of ensembles in replica_index.xvg. But I have a
> > > doubt, you said that " *At time 4, replicas in ensemble 1 and 2 have
> > > exchanged. So replica 0 is now in ensemble 2, which is expressed by 0
> in
> > > the third column*
> > > *of the third row of replica_index.xvg.* "
> > >
> > > This is fine , as the output of replica_index is :-
> > > 4   12*0 *   3456789   10   11
> > 13
> > >   12
> > >
> > > But, i didn't understand this " The same condition is expressed by the
> > > first column of the third row of replica_temp.xvg, where you will find
> 2,
> > > also expressing that replica 0 is in ensemble 2 at time 4." Here's the
> > > output for replica_temp . The first column third row is 2, its ok, but,
> > its
> > > shows that replica 0 is in ensemble 1 instead of 2.
> > >
> >
> > No, if the rows of both matrices describe time, and there are two
> different
> > matrices for the same exchange set, then the information described by a
> > column must differ, like I said last email. You are applying the same
> > interpretation to a column from either matrix.
> >
> >
> > > 4   2013456789   10   11
> 13
> > > 12
> > >
> > >
> > > In addition to this, in my last mail I showed the temp graph for all
> > > replicas. (https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png)
> .
> > > Not all replicas visit all the temperatures, but some of them visit all
> > the
> > > temperatures. Is it sufficient to move with the further analysis , as
> in
> > > some papers they show that some replicas visit all the temp which means
> > > that the sufficient sampling has been achieved. In my case this is true
> > for
> > > some of the replicas and the average acceptance ratio achieved was 0.22
> > ??
> > >
> >
> > I've answered this question several times. Each replica merely visiting
> > each temperature means nothing for converged sampling. There's lots of
> > literature here, including stuff by me ;-) A balance of replicas visiting
> > ensembles is necessary but not sufficient for the kind of replica flow
> that
> > would be necessary for generalized convergence. One can shrug one's
> > shoulders at some point and say things are probably as good as they'll
> get
> > for reasonable cost, but your reviewer might disagree with you.
> Convergence
> > of sampling at a single temperature can be assessed in a similar way as
> for
> > non-REMD simulations, caveat that the exchange events pretty much stop
> you
> > using metrics based on correlation time. If you want to know how to do
> > things properly, you need to do some reading.
> >
> > Mark
> >
> >
> > >
> > >
> > >
> > > On Fri, May 24, 2013 at 5:07 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> > > >wrote:
> > >
> > > > At time 0 we have an set of replicas and an (ordered) set of
> ensembles.
> > > We
> > > > could label these however we liked, but for (in)convenience we use
> > > 0-(n-1)
> > > > for both. The rows of the matrices in the *.xvg files change with
> time.
> > > At
> > > > time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is
> > now
> > > in
> > > > ensemble 1. At time 4, replicas in ensemble 1 and 2 have exchanged.
> So
> > > > replica 0 is now in ensemble 2, which is expressed by 0 in the third
> > > column
> > > > of the third row of replica_index.xvg. The same condition is
> expressed
> > by
> > > > the first column of the third row of replica_temp.xvg, where you will
> > > find
> > > > 2, also expressing that replica 0 is in ensemble 2 at time 4. The
> > columns
> > > > of the two matrices allow you to see either the profile of which
> > replica
> > > > was in this ensemble at which time, or which ensemble this replica
> was
> > in
> > > > at which time.
> > > >
> > > > Mark
> > > >
> > > >
> > > > On Fri, May 24, 2013 at 8:43 AM, bharat gupta <
> > bharat.85.m...@gmail.com
> > > > >wrote:
> > > >
> > > > > Dear Sir,
> > > > >
> > > > > I tried a lot to understand the meaning a

Re: [gmx-users] the "-dist" flag of g_hbond tool

[Erik Marklund]

Hi,

See below

On 24 May 2013, at 11:45, CHEN Pan  wrote:

> Dear Gromacs users,
> 
> I am confused about the g_hbond tools.
> 
> 1) When I use "-dist" to get the distribution of hydrogen bonding distance,
> I found that the summation of the population is always 200 (the y-column
> below). I am not sure if it's was done with normalization or not, if yes,
> the summation should be one, if no, then the summation should equals to the
> total number of the hydrogen bonds, but here the "hbnum.xvg" shows me I
> have 440 hydrogen bonds. Why here is always 200, not matter what types of
> hydrogen bonds.

How many donors do you have, and how many acceptors?

> 
> 2) In my system, there are several different types of hydrogen bonds, such
> as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen
> bonds. Is there any "smart" way to separately calculate those hydrogen
> bonds? By using the "index.ndx" file, I could separate the intra-chain
> hydrogen bonds, then I can get the inter-chain ones using the total one
> minus the intra-chain one. It may be possible to do the same for the
> intra-sheet and the inter-sheet. However, this strategy seems "complex".
> Did anybody have experience or ideas for this problem?
> 
> Pan
> 
> # This file was created Fri May 24 11:06:01 2013
> # by the following command:
> # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s
> /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b 11000 -e
> 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g
> #
> # g_hbond is part of G R O M A C S:
> #
> # Gromacs Runs One Microsecond At Cannonball Speeds
> #
> @title "Hydrogen Bond Distribution"
> @xaxis  label "Hydrogen - Acceptor Distance (nm)"
> @yaxis  label ""
> @TYPE xy
>0.0025  0
>0.0075  0
>0.0125  0
>0.0175  0
>0.0225  0
>0.0275  0
>0.0325  0
>0.0375  0
>0.0425  0
>0.0475  0
>0.0525  0
>0.0575  0
>0.0625  0
>0.0675  0
>0.0725  0
>0.0775  0
>0.0825  0
>0.0875  0
>0.0925  0
>0.0975  0
>0.1025  0
>0.1075  0
>0.1125  0
>0.1175  0
>0.1225  0
>0.1275  0
>0.1325  0
>0.1375  0
>0.1425  0
>0.1475  0
>0.1525  0
>0.1575  0
>0.1625  0
>0.1675  0
>0.1725  0
>0.1775  0
>0.1825  0
>0.1875  0
>0.1925  0
>0.1975  0
>0.2025  0
>0.2075  0
>0.2125  0
>0.2175  0
>0.2225  0
>0.2275  0
>0.2325 0.00538632
>0.2375   0.125501
>0.24251.23562
>0.24756.08295
>0.252516.4279
>0.257528.6597
>0.262536.0576
>0.2675 35.154
>0.272528.1539
>0.277519.8073
>0.282512.4602
>0.28757.23832
>0.29254.06577
>0.29752.15794
>0.30251.14423
>0.3075   0.588366
>0.3125   0.310611
>0.3175   0.163206
>0.3225  0.0772039
>0.3275  0.0411156
>0.3325  0.0210066
>0.3375  0.0113113
>0.3425 0.00574541
>0.3475 0.00502723
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[gmx-users] GPU-based workstation

[James Starlight]

Dear Gromacs Users!


I'd like to build new workstation for performing simulation on GPU with
Gromacs 4.6 native cuda support.
Recently I've used such setup with  Core i5 cpu and nvidia 670 GTX video
and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system
with SD integrator)


Now I'd like to build multi-gpu wokstation.

My question - How much GPU would give me best performance on the typical
home-like workstation. What algorithm of Ncidia GPU integration should I
use (e.g SLI etc) ?


Thanks for help,


James
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Re: [gmx-users] REMD:subsystems are not compatible.

[Mark Abraham]

Depends what's in the _prev files.

The original problem might be http://redmine.gromacs.org/issues/801, in
which case you should try 4.5.6


On Fri, May 24, 2013 at 1:01 PM, suhani nagpal wrote:

> Hello Mark
>
> Thanks for the suggestions.
>
> I used gmxcheck on my _prev.cpt files, they all show last time step - 7.3
> ns
>
> but when I resume remd with _prev.cpt files , it's starting from 0 ps.
>
> Did i miss something ?
>
>
> On Fri, May 24, 2013 at 3:37 PM, Mark Abraham  >wrote:
>
> > Probably your set of state_.cpt files is mutually inconsistent after some
> > crash, because some files were written and some were not. Use gmxcheck to
> > find out the times. The good news is that the _prev.cpt files will allow
> > you to construct a self-consistent set.
> >
> > Mark
> >
> >
> > On Fri, May 24, 2013 at 11:36 AM, suhani nagpal  > >wrote:
> >
> > > Greetings
> > >
> > > I'm running REMD with 96 replicas.
> > > It has run till 7.3 ns after extending it once using
> > >
> > > mdrun_mpi -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend
> > >
> > >
> > > And if i put to restart this again it shows the error:
> > >
> > > ---
> > > Program mdrun_mpi, VERSION 4.5.5
> > > Source code file: main.c, line: 249
> > >
> > > Fatal error:
> > > The 96 subsystems are not compatible.
> > >
> > >
> > > Kindly assist me regarding this.
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > Suhani
> > > SRF
> > > CSIR-IGIB, India
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > > www interface or send it to gmx-users-requ...@gromacs.org.
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> > >
> > --
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> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
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Re: [gmx-users] REMD:subsystems are not compatible.

[suhani nagpal]

Hello Mark

Thanks for the suggestions.

I used gmxcheck on my _prev.cpt files, they all show last time step - 7.3 ns

but when I resume remd with _prev.cpt files , it's starting from 0 ps.

Did i miss something ?


On Fri, May 24, 2013 at 3:37 PM, Mark Abraham wrote:

> Probably your set of state_.cpt files is mutually inconsistent after some
> crash, because some files were written and some were not. Use gmxcheck to
> find out the times. The good news is that the _prev.cpt files will allow
> you to construct a self-consistent set.
>
> Mark
>
>
> On Fri, May 24, 2013 at 11:36 AM, suhani nagpal  >wrote:
>
> > Greetings
> >
> > I'm running REMD with 96 replicas.
> > It has run till 7.3 ns after extending it once using
> >
> > mdrun_mpi -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend
> >
> >
> > And if i put to restart this again it shows the error:
> >
> > ---
> > Program mdrun_mpi, VERSION 4.5.5
> > Source code file: main.c, line: 249
> >
> > Fatal error:
> > The 96 subsystems are not compatible.
> >
> >
> > Kindly assist me regarding this.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > Suhani
> > SRF
> > CSIR-IGIB, India
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
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Re: [gmx-users] Re: REMD analysis

[francesco oteri]

Hi to everybody,
Bharat, maybe i didn't follow exactly the wole tale, but is it possible you
are running xmgrace without the -nxy option?
You are probably visualizing the data related the 1st replica several times!

Francesco


2013/5/24 Mark Abraham 

> On Fri, May 24, 2013 at 10:44 AM, bharat gupta  >wrote:
>
> > Dear Sir,
> >
> > Thank you for your detailed response to my query. I understood the
> concept
> > of ordered arrangement of ensembles in replica_index.xvg. But I have a
> > doubt, you said that " *At time 4, replicas in ensemble 1 and 2 have
> > exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in
> > the third column*
> > *of the third row of replica_index.xvg.* "
> >
> > This is fine , as the output of replica_index is :-
> > 4   12*0 *   3456789   10   11
> 13
> >   12
> >
> > But, i didn't understand this " The same condition is expressed by the
> > first column of the third row of replica_temp.xvg, where you will find 2,
> > also expressing that replica 0 is in ensemble 2 at time 4." Here's the
> > output for replica_temp . The first column third row is 2, its ok, but,
> its
> > shows that replica 0 is in ensemble 1 instead of 2.
> >
>
> No, if the rows of both matrices describe time, and there are two different
> matrices for the same exchange set, then the information described by a
> column must differ, like I said last email. You are applying the same
> interpretation to a column from either matrix.
>
>
> > 4   2013456789   10   11   13
> > 12
> >
> >
> > In addition to this, in my last mail I showed the temp graph for all
> > replicas. (https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png) .
> > Not all replicas visit all the temperatures, but some of them visit all
> the
> > temperatures. Is it sufficient to move with the further analysis , as in
> > some papers they show that some replicas visit all the temp which means
> > that the sufficient sampling has been achieved. In my case this is true
> for
> > some of the replicas and the average acceptance ratio achieved was 0.22
> ??
> >
>
> I've answered this question several times. Each replica merely visiting
> each temperature means nothing for converged sampling. There's lots of
> literature here, including stuff by me ;-) A balance of replicas visiting
> ensembles is necessary but not sufficient for the kind of replica flow that
> would be necessary for generalized convergence. One can shrug one's
> shoulders at some point and say things are probably as good as they'll get
> for reasonable cost, but your reviewer might disagree with you. Convergence
> of sampling at a single temperature can be assessed in a similar way as for
> non-REMD simulations, caveat that the exchange events pretty much stop you
> using metrics based on correlation time. If you want to know how to do
> things properly, you need to do some reading.
>
> Mark
>
>
> >
> >
> >
> > On Fri, May 24, 2013 at 5:07 PM, Mark Abraham  > >wrote:
> >
> > > At time 0 we have an set of replicas and an (ordered) set of ensembles.
> > We
> > > could label these however we liked, but for (in)convenience we use
> > 0-(n-1)
> > > for both. The rows of the matrices in the *.xvg files change with time.
> > At
> > > time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is
> now
> > in
> > > ensemble 1. At time 4, replicas in ensemble 1 and 2 have exchanged. So
> > > replica 0 is now in ensemble 2, which is expressed by 0 in the third
> > column
> > > of the third row of replica_index.xvg. The same condition is expressed
> by
> > > the first column of the third row of replica_temp.xvg, where you will
> > find
> > > 2, also expressing that replica 0 is in ensemble 2 at time 4. The
> columns
> > > of the two matrices allow you to see either the profile of which
> replica
> > > was in this ensemble at which time, or which ensemble this replica was
> in
> > > at which time.
> > >
> > > Mark
> > >
> > >
> > > On Fri, May 24, 2013 at 8:43 AM, bharat gupta <
> bharat.85.m...@gmail.com
> > > >wrote:
> > >
> > > > Dear Sir,
> > > >
> > > > I tried a lot to understand the meaning and relation between the .log
> > > file
> > > > and relica_index file, but I was not able to break the code. I tried
> to
> > > > look into gmx forum for some clue, but didn't find any. So, if
> possible
> > > can
> > > > you explain it ...
> > > >
> > > > Replica exchange at step 1000 time 2
> > > > Repl 0 <-> 1  dE = -1.067e+00
> > > > Repl ex  0 x  123456789   10   11
> 12
> > x
> > > 13
> > > > Repl pr   1.0   .01   .68   .21   .05   .09
> > .26
> > > >
> > > >
> > > > Replica exchange at step 2000 time 4
> > > > Repl ex  01 x  23456789   10   11
> 12
> > > 13
> > > > Repl pr.91   .32   .00   .07   .18   .08
> > > >
> > > > output of replica_index.xvg
> > > >
> > > > 0   0   

Re: [gmx-users] REMD:subsystems are not compatible.

[Mark Abraham]

Probably your set of state_.cpt files is mutually inconsistent after some
crash, because some files were written and some were not. Use gmxcheck to
find out the times. The good news is that the _prev.cpt files will allow
you to construct a self-consistent set.

Mark


On Fri, May 24, 2013 at 11:36 AM, suhani nagpal wrote:

> Greetings
>
> I'm running REMD with 96 replicas.
> It has run till 7.3 ns after extending it once using
>
> mdrun_mpi -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend
>
>
> And if i put to restart this again it shows the error:
>
> ---
> Program mdrun_mpi, VERSION 4.5.5
> Source code file: main.c, line: 249
>
> Fatal error:
> The 96 subsystems are not compatible.
>
>
> Kindly assist me regarding this.
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Suhani
> SRF
> CSIR-IGIB, India
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
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>
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Re: [gmx-users] Re: REMD analysis

[Mark Abraham]

On Fri, May 24, 2013 at 10:44 AM, bharat gupta wrote:

> Dear Sir,
>
> Thank you for your detailed response to my query. I understood the concept
> of ordered arrangement of ensembles in replica_index.xvg. But I have a
> doubt, you said that " *At time 4, replicas in ensemble 1 and 2 have
> exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in
> the third column*
> *of the third row of replica_index.xvg.* "
>
> This is fine , as the output of replica_index is :-
> 4   12*0 *   3456789   10   11   13
>   12
>
> But, i didn't understand this " The same condition is expressed by the
> first column of the third row of replica_temp.xvg, where you will find 2,
> also expressing that replica 0 is in ensemble 2 at time 4." Here's the
> output for replica_temp . The first column third row is 2, its ok, but, its
> shows that replica 0 is in ensemble 1 instead of 2.
>

No, if the rows of both matrices describe time, and there are two different
matrices for the same exchange set, then the information described by a
column must differ, like I said last email. You are applying the same
interpretation to a column from either matrix.


> 4   2013456789   10   11   13
> 12
>
>
> In addition to this, in my last mail I showed the temp graph for all
> replicas. (https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png) .
> Not all replicas visit all the temperatures, but some of them visit all the
> temperatures. Is it sufficient to move with the further analysis , as in
> some papers they show that some replicas visit all the temp which means
> that the sufficient sampling has been achieved. In my case this is true for
> some of the replicas and the average acceptance ratio achieved was 0.22 ??
>

I've answered this question several times. Each replica merely visiting
each temperature means nothing for converged sampling. There's lots of
literature here, including stuff by me ;-) A balance of replicas visiting
ensembles is necessary but not sufficient for the kind of replica flow that
would be necessary for generalized convergence. One can shrug one's
shoulders at some point and say things are probably as good as they'll get
for reasonable cost, but your reviewer might disagree with you. Convergence
of sampling at a single temperature can be assessed in a similar way as for
non-REMD simulations, caveat that the exchange events pretty much stop you
using metrics based on correlation time. If you want to know how to do
things properly, you need to do some reading.

Mark


>
>
>
> On Fri, May 24, 2013 at 5:07 PM, Mark Abraham  >wrote:
>
> > At time 0 we have an set of replicas and an (ordered) set of ensembles.
> We
> > could label these however we liked, but for (in)convenience we use
> 0-(n-1)
> > for both. The rows of the matrices in the *.xvg files change with time.
> At
> > time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is now
> in
> > ensemble 1. At time 4, replicas in ensemble 1 and 2 have exchanged. So
> > replica 0 is now in ensemble 2, which is expressed by 0 in the third
> column
> > of the third row of replica_index.xvg. The same condition is expressed by
> > the first column of the third row of replica_temp.xvg, where you will
> find
> > 2, also expressing that replica 0 is in ensemble 2 at time 4. The columns
> > of the two matrices allow you to see either the profile of which replica
> > was in this ensemble at which time, or which ensemble this replica was in
> > at which time.
> >
> > Mark
> >
> >
> > On Fri, May 24, 2013 at 8:43 AM, bharat gupta  > >wrote:
> >
> > > Dear Sir,
> > >
> > > I tried a lot to understand the meaning and relation between the .log
> > file
> > > and relica_index file, but I was not able to break the code. I tried to
> > > look into gmx forum for some clue, but didn't find any. So, if possible
> > can
> > > you explain it ...
> > >
> > > Replica exchange at step 1000 time 2
> > > Repl 0 <-> 1  dE = -1.067e+00
> > > Repl ex  0 x  123456789   10   11   12
> x
> > 13
> > > Repl pr   1.0   .01   .68   .21   .05   .09
> .26
> > >
> > >
> > > Replica exchange at step 2000 time 4
> > > Repl ex  01 x  23456789   10   11   12
> > 13
> > > Repl pr.91   .32   .00   .07   .18   .08
> > >
> > > output of replica_index.xvg
> > >
> > > 0   0123456789   10   11
> 12
> > > 13
> > > 2   1023456789   10   11
> 13
> > > 12
> > > 4   1203456789   10   11
> 13
> > > 12
> > >
> > > On Thu, May 23, 2013 at 11:20 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> > > >wrote:
> > >
> > > > Looked fine
> > > >
> > > >
> > > > On Thu, May 23, 2013 at 4:13 PM, bharat gupta <
> > bharat.85.m...@gmail.com
> > > > >wrote:
> > > >
> > > > > Sir,
> > > > >
> > 

[gmx-users] the "-dist" flag of g_hbond tool

[CHEN Pan]

Dear Gromacs users,

I am confused about the g_hbond tools.

1) When I use "-dist" to get the distribution of hydrogen bonding distance,
I found that the summation of the population is always 200 (the y-column
below). I am not sure if it's was done with normalization or not, if yes,
the summation should be one, if no, then the summation should equals to the
total number of the hydrogen bonds, but here the "hbnum.xvg" shows me I
have 440 hydrogen bonds. Why here is always 200, not matter what types of
hydrogen bonds.

2) In my system, there are several different types of hydrogen bonds, such
as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen
bonds. Is there any "smart" way to separately calculate those hydrogen
bonds? By using the "index.ndx" file, I could separate the intra-chain
hydrogen bonds, then I can get the inter-chain ones using the total one
minus the intra-chain one. It may be possible to do the same for the
intra-sheet and the inter-sheet. However, this strategy seems "complex".
Did anybody have experience or ideas for this problem?

Pan

# This file was created Fri May 24 11:06:01 2013
# by the following command:
# g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s
/Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b 11000 -e
16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g
#
# g_hbond is part of G R O M A C S:
#
# Gromacs Runs One Microsecond At Cannonball Speeds
#
@title "Hydrogen Bond Distribution"
@xaxis  label "Hydrogen - Acceptor Distance (nm)"
@yaxis  label ""
@TYPE xy
0.0025  0
0.0075  0
0.0125  0
0.0175  0
0.0225  0
0.0275  0
0.0325  0
0.0375  0
0.0425  0
0.0475  0
0.0525  0
0.0575  0
0.0625  0
0.0675  0
0.0725  0
0.0775  0
0.0825  0
0.0875  0
0.0925  0
0.0975  0
0.1025  0
0.1075  0
0.1125  0
0.1175  0
0.1225  0
0.1275  0
0.1325  0
0.1375  0
0.1425  0
0.1475  0
0.1525  0
0.1575  0
0.1625  0
0.1675  0
0.1725  0
0.1775  0
0.1825  0
0.1875  0
0.1925  0
0.1975  0
0.2025  0
0.2075  0
0.2125  0
0.2175  0
0.2225  0
0.2275  0
0.2325 0.00538632
0.2375   0.125501
0.24251.23562
0.24756.08295
0.252516.4279
0.257528.6597
0.262536.0576
0.2675 35.154
0.272528.1539
0.277519.8073
0.282512.4602
0.28757.23832
0.29254.06577
0.29752.15794
0.30251.14423
0.3075   0.588366
0.3125   0.310611
0.3175   0.163206
0.3225  0.0772039
0.3275  0.0411156
0.3325  0.0210066
0.3375  0.0113113
0.3425 0.00574541
0.3475 0.00502723
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[gmx-users] REMD:subsystems are not compatible.

[suhani nagpal]

Greetings

I'm running REMD with 96 replicas.
It has run till 7.3 ns after extending it once using

mdrun_mpi -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend


And if i put to restart this again it shows the error:

---
Program mdrun_mpi, VERSION 4.5.5
Source code file: main.c, line: 249

Fatal error:
The 96 subsystems are not compatible.


Kindly assist me regarding this.
















Suhani
SRF
CSIR-IGIB, India
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Re: [gmx-users] Re: REMD analysis

[bharat gupta]

Dear Sir,

Thank you for your detailed response to my query. I understood the concept
of ordered arrangement of ensembles in replica_index.xvg. But I have a
doubt, you said that " *At time 4, replicas in ensemble 1 and 2 have
exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in
the third column*
*of the third row of replica_index.xvg.* "

This is fine , as the output of replica_index is :-
4   12*0 *   3456789   10   11   13
  12

But, i didn't understand this " The same condition is expressed by the
first column of the third row of replica_temp.xvg, where you will find 2,
also expressing that replica 0 is in ensemble 2 at time 4." Here's the
output for replica_temp . The first column third row is 2, its ok, but, its
shows that replica 0 is in ensemble 1 instead of 2.

4   2013456789   10   11   13
12


In addition to this, in my last mail I showed the temp graph for all
replicas. (https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png) .
Not all replicas visit all the temperatures, but some of them visit all the
temperatures. Is it sufficient to move with the further analysis , as in
some papers they show that some replicas visit all the temp which means
that the sufficient sampling has been achieved. In my case this is true for
some of the replicas and the average acceptance ratio achieved was 0.22 ??



On Fri, May 24, 2013 at 5:07 PM, Mark Abraham wrote:

> At time 0 we have an set of replicas and an (ordered) set of ensembles. We
> could label these however we liked, but for (in)convenience we use 0-(n-1)
> for both. The rows of the matrices in the *.xvg files change with time. At
> time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is now in
> ensemble 1. At time 4, replicas in ensemble 1 and 2 have exchanged. So
> replica 0 is now in ensemble 2, which is expressed by 0 in the third column
> of the third row of replica_index.xvg. The same condition is expressed by
> the first column of the third row of replica_temp.xvg, where you will find
> 2, also expressing that replica 0 is in ensemble 2 at time 4. The columns
> of the two matrices allow you to see either the profile of which replica
> was in this ensemble at which time, or which ensemble this replica was in
> at which time.
>
> Mark
>
>
> On Fri, May 24, 2013 at 8:43 AM, bharat gupta  >wrote:
>
> > Dear Sir,
> >
> > I tried a lot to understand the meaning and relation between the .log
> file
> > and relica_index file, but I was not able to break the code. I tried to
> > look into gmx forum for some clue, but didn't find any. So, if possible
> can
> > you explain it ...
> >
> > Replica exchange at step 1000 time 2
> > Repl 0 <-> 1  dE = -1.067e+00
> > Repl ex  0 x  123456789   10   11   12 x
> 13
> > Repl pr   1.0   .01   .68   .21   .05   .09   .26
> >
> >
> > Replica exchange at step 2000 time 4
> > Repl ex  01 x  23456789   10   11   12
> 13
> > Repl pr.91   .32   .00   .07   .18   .08
> >
> > output of replica_index.xvg
> >
> > 0   0123456789   10   11   12
> > 13
> > 2   1023456789   10   11   13
> > 12
> > 4   1203456789   10   11   13
> > 12
> >
> > On Thu, May 23, 2013 at 11:20 PM, Mark Abraham  > >wrote:
> >
> > > Looked fine
> > >
> > >
> > > On Thu, May 23, 2013 at 4:13 PM, bharat gupta <
> bharat.85.m...@gmail.com
> > > >wrote:
> > >
> > > > Sir,
> > > >
> > > > What about the description of replica_temp file that I posted in last
> > > mail.
> > > > I think that's correct ... If you can comment on that, I can move on
> > with
> > > > replica_index file...
> > > >
> > > >
> > > > On Thu, May 23, 2013 at 10:58 PM, Mark Abraham <
> > mark.j.abra...@gmail.com
> > > > >wrote:
> > > >
> > > > > It's a demux. One might want trajectories to be at constant
> > > temperature,
> > > > or
> > > > > constant replica. The two files define the (mutually inverse)
> > mappings
> > > > > between those representations. So one file tells you which replica
> is
> > > at
> > > > > each temperature, and the other which temperature holds each
> replica.
> > > > > Nobody's ever written down anything about which is which, so like I
> > > said
> > > > a
> > > > > week back, look at the first few exchanges, see how those are
> > > represented
> > > > > in the files, and decide for yourself which file's columns/rows
> have
> > > > useful
> > > > > information you want to look at. And do write that decision down!
> :-)
> > > > >
> > > > > Mark
> > > > >
> > > > >
> > > > > On Thu, May 23, 2013 at 2:55 PM, simula_460 <
> > bharat.85.m...@gmail.com
> > > > > >wrote:
> > > > >
> > > > > > I checked the md.log and replica_temp.xvg file , what I
> understood
> > is
> > > > > that
> > > > > > the 'x' mean

Re: [gmx-users] Re: REMD analysis

[Mark Abraham]

At time 0 we have an set of replicas and an (ordered) set of ensembles. We
could label these however we liked, but for (in)convenience we use 0-(n-1)
for both. The rows of the matrices in the *.xvg files change with time. At
time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is now in
ensemble 1. At time 4, replicas in ensemble 1 and 2 have exchanged. So
replica 0 is now in ensemble 2, which is expressed by 0 in the third column
of the third row of replica_index.xvg. The same condition is expressed by
the first column of the third row of replica_temp.xvg, where you will find
2, also expressing that replica 0 is in ensemble 2 at time 4. The columns
of the two matrices allow you to see either the profile of which replica
was in this ensemble at which time, or which ensemble this replica was in
at which time.

Mark


On Fri, May 24, 2013 at 8:43 AM, bharat gupta wrote:

> Dear Sir,
>
> I tried a lot to understand the meaning and relation between the .log file
> and relica_index file, but I was not able to break the code. I tried to
> look into gmx forum for some clue, but didn't find any. So, if possible can
> you explain it ...
>
> Replica exchange at step 1000 time 2
> Repl 0 <-> 1  dE = -1.067e+00
> Repl ex  0 x  123456789   10   11   12 x 13
> Repl pr   1.0   .01   .68   .21   .05   .09   .26
>
>
> Replica exchange at step 2000 time 4
> Repl ex  01 x  23456789   10   11   12   13
> Repl pr.91   .32   .00   .07   .18   .08
>
> output of replica_index.xvg
>
> 0   0123456789   10   11   12
> 13
> 2   1023456789   10   11   13
> 12
> 4   1203456789   10   11   13
> 12
>
> On Thu, May 23, 2013 at 11:20 PM, Mark Abraham  >wrote:
>
> > Looked fine
> >
> >
> > On Thu, May 23, 2013 at 4:13 PM, bharat gupta  > >wrote:
> >
> > > Sir,
> > >
> > > What about the description of replica_temp file that I posted in last
> > mail.
> > > I think that's correct ... If you can comment on that, I can move on
> with
> > > replica_index file...
> > >
> > >
> > > On Thu, May 23, 2013 at 10:58 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> > > >wrote:
> > >
> > > > It's a demux. One might want trajectories to be at constant
> > temperature,
> > > or
> > > > constant replica. The two files define the (mutually inverse)
> mappings
> > > > between those representations. So one file tells you which replica is
> > at
> > > > each temperature, and the other which temperature holds each replica.
> > > > Nobody's ever written down anything about which is which, so like I
> > said
> > > a
> > > > week back, look at the first few exchanges, see how those are
> > represented
> > > > in the files, and decide for yourself which file's columns/rows have
> > > useful
> > > > information you want to look at. And do write that decision down! :-)
> > > >
> > > > Mark
> > > >
> > > >
> > > > On Thu, May 23, 2013 at 2:55 PM, simula_460 <
> bharat.85.m...@gmail.com
> > > > >wrote:
> > > >
> > > > > I checked the md.log and replica_temp.xvg file , what I understood
> is
> > > > that
> > > > > the 'x' means swapping and replica are written this way.
> > > > > For eg.
> > > > > Replica exchange at step 1000 time 2
> > > > > Repl 0 <-> 1  dE = -1.067e+00
> > > > > Repl ex  0 x  123456789   10   11
> > 12
> > > x
> > > > 13
> > > > > Repl pr   1.0   .01   .68   .21   .05   .09
> > > .26
> > > > >
> > > > > output in replica_temp file will be
> > > > > 1 0 2 3 4 5 6 7 8 9 10 11 13 12
> > > > >
> > > > > It means that replica 1 at higher temp. exchange with the one in
> > lower
> > > > temp
> > > > > 0.
> > > > >
> > > > > Replica exchange at step 2000 time 4
> > > > > Repl ex  01 x  23456789   10   11
> > 12
> > > > 13
> > > > > Repl pr.91   .32   .00   .07   .18
> .08
> > > > >
> > > > > output in replica_temp file will be
> > > > > 1 0 2 3 4 5 6 7 8 9 10 11 13 12
> > > > > 2 0 1 3 4 5 6 7 8 9 10 11 13 12
> > > > >
> > > > > [order is from low to high temp]
> > > > >
> > > > > But I am not able to understand for replica_index file :-
> > > > >
> > > > > for the above two time steps here's the output :-
> > > > > 0   0123456789   10
> 11
> > > 12
> > > > > 13
> > > > > 2   1023456789   10
> 11
> > > 13
> > > > > 12
> > > > > 4   1203456789   10
> 11
> > > 13
> > > > > 12
> > > > >
> > > > > The time step four is different here, I don't know why ?? Ideally
> the
> > > > > output should be same in both files, I suppose ??
> > > > >
> > > > > Also, I tried to plot for each column separately , here I want to
> > > clarify
> > > > > that whether each column represents

Re: [gmx-users] g_hbond

[Erik Marklund]

Hi,

Just to clarify: The third column are the number of acceptor-donor pairs that 
fulfil the distance criterion but not the angle criterion.

Erik

On 24 May 2013, at 09:06, CHEN Pan  wrote:

> Hi Maggin,
> The middle column is the total number of hydrogen bonds in your system
> under the definition of the hydrogen bonds criteria you have defined (here
> you used the default value). The third column is the number of
> acceptor-donor paris in the system. The first column is the simulation
> time, your trajectory file are saved every 2 ps right?
> If you use "xmgrace bovin_hnum.xvg", you can easily find what's the meaning
> of the second and third column.
> 
> Pan
> 
> 2013/5/24 maggin 
> 
>> # This file was created Fri May 24 13:03:14 2013
>> # by the following command:
>> # g_hbond -f traj_all_md.trr -s md_0_1_next1.tpr -num bovin_hnum.xvg
>> #
>> # g_hbond is part of G R O M A C S:
>> #
>> # Green Red Orange Magenta Azure Cyan Skyblue
>> #
>> @title "Hydrogen Bonds"
>> @xaxis  label "Time (ps)"
>> @yaxis  label "Number"
>> @TYPE xy
>> @ view 0.15, 0.15, 0.75, 0.85
>> @ legend on
>> @ legend box on
>> @ legend loctype view
>> @ legend 0.78, 0.8
>> @ legend length 2
>> @ s0 legend "Hydrogen bonds"
>> @ s1 legend "Pairs within 0.35 nm"
>> 0  74 517
>> 2  73 515
>> 4  69 515
>> 6  69 529
>> 8  78 525
>>10  74 517
>>12  68 516
>>14  68 524
>>16  71 520
>>   
>> hi, anybody can tell me at here if Hydrogen bonds Refers to the middle
>> column: 74,73,69,69,78,74,68,68,71
>> 
>> Thank you !
>> 
>> maggin
>> 
>> 
>> 
>> 
>> --
>> View this message in context:
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Re: [gmx-users] Have your ever got a real NVE simulation (good energy conservation) in gromacs?

[Erik Marklund]

Hi,

I have achieved good energy conservation in NVE simulations. This was single 
proteins in the gas phase, using infinite cut-offs, constraints applied to 
hydrogens, 0.5 fs or 1.0 fs time steps, double precision and virtual sites if 
I'm not mistaken. We had problems with energy conservation for the first 
publication (Patriksson et al 2007, Biochemistry. The methods section states 
1.0 fs, but that's a typo for we used 0.5 fs) for 1.0 fs time steps. For a 
second publication (Marklund et al 2009, PCCP) 1.0 fs worked fine, using a 
later gromacs version. In the first case we used SHAKE and in the later LINCS I 
think.

Hope that helps

Erik

On 23 May 2013, at 23:59, cyberjhon  wrote:

> Hi Guys
> 
> I have been trying by all means to get a real good Energy conservation in
> NVE simulations using gromacs
> but it has been almost impossible for me. 
> I have tried many different combinations of Coulomb and VdW parameters and
> changed the cut off radius and nothing.
> 1. Have you ever obtained energy conservation in Gromacs?
> 2. Under what conditions ? for what system? 
> 2. Do you have a set of parameters that works to obtain energy conservation?
> if you can share with me the mdp file, I will appreciate it.
> My system is Human Papiloma Virus  virus-like particle T=1 inmersed in SPC
> water.
> 
> Thanks
> 
> John Michael Espinsoa Duran
> 
> 
> 
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/Have-your-ever-got-a-real-NVE-simulation-good-energy-conservation-in-gromacs-tp5008501.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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[gmx-users] Re: residue labeling in g_rmsf

[maggin]

Hi, you can use Matlab software to do it!

maggin



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[gmx-users] Re: g_hbond

[maggin]

Hi, Pan

Thank you very much for your kind help! Thank you!

maggin



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Re: [gmx-users] residue labeling in g_rmsf

[Tsjerk Wassenaar]

Hi Arunima,

In bash you can also combine the residue names and such with the RMSF graph:

paste <(grep "^\(ATOM\|HETATM\)" structure.pdb | cut -b 17-26 | uniq)
<(grep "^[^#@]" rmsf.xvg)

To make it a bit more clear, the redirection <( ... ) treats the output of
the command between parentheses as an input file, so we paste the results
from two commands. The first command extracts the atom residue and chain
info and uniqifies, giving a list of residues. The second command strips
the metadata fram the xvg file.

Hope it helps,

Tsjerk



On Thu, May 23, 2013 at 1:52 PM, Justin Lemkul  wrote:

>
>
> On 5/23/13 6:51 AM, Arunima Shilpi wrote:
>
>> Respected Sir
>>
>> If i want my residue  name to be labeled in the graph for g_rmsf ,how
>> should I proceed...
>>
>> I used the following command
>>
>> g_rmsf -f md_0_1.xtc -s md_0_1.tpr -res -o  rmsf.xvg
>>
>>
> Add labels in your favorite plotting software.  g_rmsf will not write
> residue names.
>
> -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] Re: Have your ever got a real NVE simulation (good energy conservation) in gromacs?

[S. Alireza Bagherzadeh]

Hi John,

I was dealing with this issue recently. Have you considered these points?

   1. Run gromacs in double-precision (mdrun_d)
   2. use PME-Switch for the treatment of the Coulombic interaction
   3. follow the guidelines from here:
   http://www.gromacs.org/Documentation/Terminology/NVE




Regards,
-- 
*S. Alireza Bagherzadeh, M.A.Sc. 
*
**
*PhD Candidate
*
**
*Dept. of Chem. & Bio. Eng. *
**
*University of BC 
*





On Thu, May 23, 2013 at 11:34 PM,  wrote:

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> Today's Topics:
>
>1. Re:The effect of coulomb-modifier and vdw-modifier in Verlet
>   cutoff scheme (Bin Liu)
>2. Re: file not found (Humayun Arafat)
>3.
> Have your ever got a real NVE simulation (good energy
>   conservation) in gromacs? (cyberjhon)
>4. On using CO2 as solvent (Bao Kai)
>5. Re: On using CO2 as solvent (Justin Lemkul)
>6. tpr of extend simulation (maggin)
>7. Re: Have your ever got a real NVE simulation (good energy
>   conservation) in gromacs? (Mark Abraham)
>8. g_hbond (maggin)
>
>
> --
>
>
>
> Message: 3
> Date: Thu, 23 May 2013 14:59:11 -0700 (PDT)
> From: cyberjhon 
> Subject: [gmx-users] Have your ever got a real NVE simulation (good
> energy conservation) in gromacs?
> To: gmx-users@gromacs.org
> Message-ID: <1369346351811-5008501.p...@n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Guys
>
> I have been trying by all means to get a real good Energy conservation in
> NVE simulations using gromacs
> but it has been almost impossible for me.
> I have tried many different combinations of Coulomb and VdW parameters and
> changed the cut off radius and nothing.
> 1. Have you ever obtained energy conservation in Gromacs?
> 2. Under what conditions ? for what system?
> 2. Do you have a set of parameters that works to obtain energy
> conservation?
> if you can share with me the mdp file, I will appreciate it.
> My system is Human Papiloma Virus  virus-like particle T=1 inmersed in SPC
> water.
>
> Thanks
>
> John Michael Espinsoa Duran
>
>
>
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Re: [gmx-users] g_hbond

[CHEN Pan]

Hi Maggin,
The middle column is the total number of hydrogen bonds in your system
under the definition of the hydrogen bonds criteria you have defined (here
you used the default value). The third column is the number of
acceptor-donor paris in the system. The first column is the simulation
time, your trajectory file are saved every 2 ps right?
If you use "xmgrace bovin_hnum.xvg", you can easily find what's the meaning
of the second and third column.

Pan

2013/5/24 maggin 

> # This file was created Fri May 24 13:03:14 2013
> # by the following command:
> # g_hbond -f traj_all_md.trr -s md_0_1_next1.tpr -num bovin_hnum.xvg
> #
> # g_hbond is part of G R O M A C S:
> #
> # Green Red Orange Magenta Azure Cyan Skyblue
> #
> @title "Hydrogen Bonds"
> @xaxis  label "Time (ps)"
> @yaxis  label "Number"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
>  0  74 517
>  2  73 515
>  4  69 515
>  6  69 529
>  8  78 525
> 10  74 517
> 12  68 516
> 14  68 524
> 16  71 520
>
> hi, anybody can tell me at here if Hydrogen bonds Refers to the middle
> column: 74,73,69,69,78,74,68,68,71
>
> Thank you !
>
> maggin
>
>
>
>
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