Re: [gmx-users] Re: Possible bug: energy changes with the number of nodes for energy minimization

[Szilárd Páll]

Or you can just use the git version.
--
Szilárd


On Wed, May 30, 2012 at 5:51 PM, Stephen Cox  wrote:
> Hi Justin and Mark,
>
> Thanks once again for getting back.
>
> I've found the problem - it's actually a known bug already:
>
> http://redmine.gromacs.org/issues/901
>
> The dispersion correction is multiplied my the number of processes (I found
> this after taking a closer look at my md.log files to see where the energy
> was changing)! I guess this means I should use the serial version for
> meaningful binding energies. It also looks like it will be fixed for version
> 4.5.6
>
> Thank you again, I really appreciate your help.
>
> Steve
>
>
>>
>> On 30/05/2012 9:42 PM, Stephen Cox wrote:
>> > Hi Justin,
>> >
>> > Thanks for getting back and posting the links.
>> >
>> >
>> >     On 5/29/12 6:22 AM, Stephen Cox wrote:
>> >     > Hi,
>> >     >
>> >     > I'm running a number of energy minimizations on a clathrate
>> >     supercell and I get
>> >     > quite significantly different values for the total energy
>> >     depending on the
>> >     > number of mpi processes / number of threads I use. More
>> >     specifically, some
>> >     > numbers I get are:
>> >     >
>> >     > #cores      energy
>> >     > 1        -2.41936409202696e+04
>> >     > 2        -2.43726425776809e+04
>> >     > 3        -2.45516442350804e+04
>> >     > 4        -2.47003944216983e+04
>> >     >
>> >     > #threads    energy
>> >     > 1        -2.41936409202696e+04
>> >     > 2        -2.43726425776792e+04
>> >     > 3        -2.45516442350804e+04
>> >     > 4        -2.47306458924815e+04
>> >     >
>> >     >
>> >     > I'd expect some numerical noise, but these differences seem to0
>> >     large for that.
>> >
>> >     The difference is only 2%, which by MD standards, is quite good,
>> >     I'd say ;)
>> >     Consider the discussion here:
>> >
>> >
>> > I agree for MD this wouldn't be too bad, but I'd expect energy
>> > minimization to get very close to the same local minimum from a given
>> > starting configuration. The thing is I want to compute a binding curve
>> > for my clathrate and compare to DFT values for the binding energy
>> > (amongst other things), and the difference in energy between different
>> > number of cores is rather significant for this purpose.
>>
>> Given the usual roughness of the PE surface to which you are minimizing,
>> some variation in end point is expected.
>>
>>
>> >
>>
>> > Furthermore, if I only calculate the energy for nsteps = 0 (i.e. a
>> > single point energy for identical structures) I get the same trend as
>> > above (both mpi/openmp with domain/particle decomposition). Surely
>> > there shouldn't be such a large difference in energy for a single
>> > point calculation?
>>
>> nsteps = 0 is not strictly a single-point energy, since the constraints
>> act before EM step 0. mdrun -s -rerun will give a single point. This
>> probably won't change your observations. You should also be sure you're
>> making observations with the latest release (4.5.5).
>>
>>
>> If you can continue to observe this trend for more processors
>> (overallocating?), then you may have evidence of a problem - but a full
>> system description and an .mdp file will be in order also.
>>
>> Mark
>
>
>> >
>> >
>> >     http://www.gromacs.org/Documentation/Terminology/Reproducibility
>> >
>> >     To an extent, the information here may also be relevant:
>> >
>> >
>> > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation
>> >
>> >     > Before submitting a bug report, I'd like to check:
>> >     > a) if someone has seen something similar;
>> >
>> >     Sure.  Energies can be different due to a whole host of factors
>> >     (discussed
>> >     above), and MPI only complicates matters.
>> >
>> >     > b) should I just trust the serial version?
>> >
>> >     Maybe, but I don't know that there's evidence to say that any of
>> >     the above tests
>> >     are more or less accurate than the others.  What happens if you
>> >     run with mdrun
>> >     -reprod on all your tests?
>> >
>> >
>> > Running with -reprod produces the same trend as above. If it was
>> > numerical noise, I would have thought that the numbers would fluctuate
>> > around some average value, not follow a definite trend where the
>> > energy decreases with the number of cores/threads...
>> >
>> >
>> >     > c) have I simply done something stupid (grompp.mdp appended
>> > below);
>> >     >
>> >
>> >     Nope, looks fine.
>> >
>> >     -Justin
>> >
>> > Thanks again for getting back to me.
>> >
>> >
>>
>> -- next part --
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20120530/a4ed4a18/attachment-0001.html
>>
>> --
>>
>> Message: 2
>> Date: Wed, 30 May 2012 07:51:02 -0400
>> From: "Justin A. Lemkul" 
>> Subject: Re: [gmx-users] Re: Possible bug: energy changes with the
>>        number  of     

[gmx-users] umbrella windows...

[rama david]

Hi Gromacs Friends,

   I am doing Justin-Umbrella sampling tutorial...
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html

After pulling I found the Chain A is moving away from protofibril but
reaches  up to the other end of the cell..
So Is these situation Satisfy the Minimum image condition??? or Am I doing
some wrong ..???

as tutorial Says..
GROMACS calculates distances while simultaneously taking periodicity into
account. This, if you have a 10-nm box, and you pull over a distance
greater than 5.0 nm, the periodic distance becomes the reference distance
for the pulling, and this distance is actually less than 5.0 nm! This fact
will significantly affect results, since the distance you *think* you are
pulling is not what is *actually* calculated.

My Query is on  very basic concept...
 tutorial says

In this example, we will be sampling COM distances from 0.5 - 5.0 nm along
the z-axis using roughly 0.2-nm spacing. The following example commands may
or may not be literally correct (the frame numbers may differ), but will
serve as an example as to how to run grompp on separate coordinate files to
generate all 23 inputs (note as well that 23 is the amount of windows
required to obtain 0.2-nm spacing over roughly 4.5 nm;
my summary_distances.dat has following lines..

00.5011713
10.5068762
20.4948514
..
.
.
1600.6993698
so my 1st configuration will be at 0 (0.5011713) and 160 (0.69936) .Is it
right???

I choose total 28 windows instead of 23 ...So is it good or bad ???

Thank you in Advance...
With Best Wishes,
Rama David
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Re: [gmx-users] umbrella windows...

[Justin A. Lemkul]

On 6/1/12 7:25 AM, rama david wrote:

Hi Gromacs Friends,

I am doing Justin-Umbrella sampling tutorial...
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html

After pulling I found the Chain A is moving away from protofibril but reaches
up to the other end of the cell..
So Is these situation Satisfy the Minimum image condition??? or Am I doing some
wrong ..???



If you set up the box properly, there should be no minimum image violation, nor 
is it particularly relevant here.  Chain A doesn't see itself and it is several 
nm away from any other protein molecule, regardless of which periodic image is 
closest.



as tutorial Says..
GROMACS calculates distances while simultaneously taking periodicity into
account. This, if you have a 10-nm box, and you pull over a distance greater
than 5.0 nm, the periodic distance becomes the reference distance for the
pulling, and this distance is actually less than 5.0 nm! This fact will
significantly affect results, since the distance you *think* you are pulling is
not what is *actually* calculated.



This statement is not related to the minimum image convention, it is addressing 
a limitation in the pull code algorithm.



My Query is on  very basic concept...
  tutorial says

In this example, we will be sampling COM distances from 0.5 - 5.0 nm along the
z-axis using roughly 0.2-nm spacing. The following example commands may or may
not be literally correct (the frame numbers may differ), but will serve as an
example as to how to run grompp on separate coordinate files to generate all 23
inputs (note as well that 23 is the amount of windows required to obtain 0.2-nm
spacing over roughly 4.5 nm;
my summary_distances.dat has following lines..

00.5011713
10.5068762
20.4948514
..
.
.
1600.6993698
so my 1st configuration will be at 0 (0.5011713) and 160 (0.69936) .Is it 
right???



Seems reasonable.  The tutorial tells you to pick intervals of about 0.2 nm.


I choose total 28 windows instead of 23 ...So is it good or bad ???



It is unnecessary.  You'll be covering extra space that winds up just wasting 
time.  The PMF will level off long before the 5.0 nm of COM separation, which in 
itself is overkill.


-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] Incomplete frame

[Turgay Cakmak]

Hi gromacs users,


I concatenated 7 trajectory files (each one has 10ns simulation) using
"trajcat". Then, when I used "gmxcheck", I get following error.

Reading frame   0 time0.000
# Atoms  68393
Precision 0.001 (nm)
Reading frame   13000 time 26000.000
*WARNING: Incomplete frame: nr 13739 time 27478
*
But, when I check the non-concatenated files with gmxcheck, I didn't get
any problem..

I am so confused. Any suggestion will be really appreciated...

Turgay
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Re: [gmx-users] Incomplete frame

[Justin A. Lemkul]

On 6/1/12 8:02 AM, Turgay Cakmak wrote:

Hi gromacs users,
I concatenated 7 trajectory files (each one has 10ns simulation) using
"trajcat". Then, when I used "gmxcheck", I get following error.
Reading frame   0 time0.000
# Atoms  68393
Precision 0.001 (nm)
Reading frame   13000 time 26000.000
*WARNING: Incomplete frame: nr 13739 time 27478
*
But, when I check the non-concatenated files with gmxcheck, I didn't get any
problem..
I am so confused. Any suggestion will be really appreciated...


Try the concatenation again.  Perhaps a filesystem blip caused an incomplete 
frame to be written.


-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] Incomplete frame

[Turgay Cakmak]

Hi Justin,

Thank you for your quick reply. I tried to concatanete the trajectory files
4 times. Three out of four try, I got same error massage.
But it worked for the last one.. It is a weird situation.. What could cause
this?

Turgay

2012/6/1 Justin A. Lemkul 

>
>
> On 6/1/12 8:02 AM, Turgay Cakmak wrote:
>
>> Hi gromacs users,
>> I concatenated 7 trajectory files (each one has 10ns simulation) using
>> "trajcat". Then, when I used "gmxcheck", I get following error.
>> Reading frame   0 time0.000
>> # Atoms  68393
>> Precision 0.001 (nm)
>> Reading frame   13000 time 26000.000
>> *WARNING: Incomplete frame: nr 13739 time 27478
>>
>> *
>> But, when I check the non-concatenated files with gmxcheck, I didn't get
>> any
>> problem..
>> I am so confused. Any suggestion will be really appreciated...
>>
>
> Try the concatenation again.  Perhaps a filesystem blip caused an
> incomplete frame to be written.
>
> -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] Incomplete frame

[Justin A. Lemkul]

On 6/1/12 8:54 AM, Turgay Cakmak wrote:

Hi Justin,
Thank you for your quick reply. I tried to concatanete the trajectory files 4
times. Three out of four try, I got same error massage.
But it worked for the last one.. It is a weird situation.. What could cause 
this?


Sounds to me like your filesystem is unstable.  It's hard to say exactly why.

-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] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface

[Klniu]

Dear Gromacs users,

I have do simulation of surfactant at oil/water interface for a long time.
But I find it too difficult to get a reasonable interfacial tension. The
key question is the pcoupltype.

My system:

Box size:  3.0 * 3.0 * 13
> Molecule Number: decane 230, water 2041
> pcoupltype = semiisotropic

Gromacs version: 4.5.5


1. When I set compressibility = 4.5e-5 4.5e-5.  Surfactant number is 32
. The box will be shrink at x and y. At last simualion will end for a fatal
error:

One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.
For more information and tips for troubleshooting, please check the GROMACS.

2. When I add the number of surfactants to 40. compressibility = 4.5e-5
4.5e-5. The interfacial tension is -20bar/nm for two interfaces.  It is not
reasonable because it should be positive.

3. When I compressibility = 0 4.5e-5.  Surfactant number is 32. The
interfacial tension is 794bar/nm for two interfaces.


My question is:

What is the right way to simulate for this system?  My work confused me too
much.  Very appreciate for you help.

Hugh
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[gmx-users] unit conversion of a force constant

[Lara Bunte]

Hello

If I have a force constant 287 kcal/(mol * A^2), the A stands for Angstrom and 
I want to calculate this to kJ/(mol * nm^2), is it correct that I have to 
multiply 4.19/0.01 = 419 to the force constant? 


Is ithis true:  287 kcal/(mol * A^2) = 120253 kJ/(mol * nm^2)

Could this be a physical realistic value or is this a hint, that 287 kcal/(mol 
* A^2) makes no sense for a force constant?

Thanks for helping
Greetings
Lara

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[gmx-users] Re: boundaries in PMF

[Thomas Schlesier]

One comment:
If the channel is horizontal orientated, and the COM of MOL lies in the 
middle, you have two directions to go out of the channel: two the left 
side (quasi negative distance) and to the right side (quasi positive 
distance).
What happens with 'pull_geometry=distance' is, that only the distance 
between MOL and Na matters. So you get the same (positive) distance if 
you go to the left or go to the right. The resulting PMF will be for 
only half of the channel (since the are no negative distances), but it 
will be evaluated from going into both directions (since the distances 
for left and right are the same).
To distingiush if you go left or right, you would need to use 
'pull_geometry=direction/position'.
If you are 100% sure, that the system is symmetric and that the COM of 
MOL is in the middle of the channel, then your results are right. But if 
the COM of MOL is a little more to the right or left (relative to the 
middle of the channel) you would get problems. Since then the left and 
right direction are not equal.


One thing you could check is.
Make a analysis with g_wham on the windows which are on the left side of 
the center and one for the right side of the center. If everything is 
converged and the system is symmetric + COM of MOL is in the middle of 
the channel, both PMF should look the same. If they differ one or more 
of the above things are not correct.



Am 31.05.2012 22:03, schrieb gmx-users-requ...@gromacs.org:

OK,
however, just one point about your last comment:


>  I suspect this is why g_wham is finding a range of values only equal to half 
of
>  your expected reaction coordinate; it is considering only the positive
>  displacement along the reaction coordinate.

It seems like all the channel is explored, not only one half. If g_wham was 
only considering the positive displacement I should see a profile for just one 
half of the channel, shouldn?t I? and I can see a profile typical for the 
entire channel.

Rebeca.


>  Date: Thu, 31 May 2012 15:42:06 -0400
>  From:jalem...@vt.edu
>  To:gmx-users@gromacs.org
>  Subject: Re: [gmx-users] Re: boundaries in PMF
>
>
>
>  On 5/31/12 3:37 PM, Rebeca Garc?a Fandi?o wrote:

>  >  Hi,
>  >  the center of mass of my channel is at the middle of the ion channel, and 
it is
>  >  a symmetric system, so I suppose these results would be OK. Anyway, I 
will check
>  >  the options you propose.

>
>  If you are sampling regions above and below the channel/membrane, then the
>  "distance" geometry is not appropriate; you need either "direction" or 
(perhaps
>  the most flexible option) "position."  There are a number of useful 
discussions
>  on such topics in the list archive and in my umbrella sampling tutorial for 
you
>  to consider.  You can likely create a series of .tpr files from new .mdp 
files
>  with correct options to run the analysis.
>
>  I suspect this is why g_wham is finding a range of values only equal to half 
of
>  your expected reaction coordinate; it is considering only the positive
>  displacement along the reaction coordinate.
>
>  -Justin
>

>  >  Thanks a lot for all your comments!!
>  >  Best wishes,
>  >  Rebeca.
>  >
>  >>  Date: Thu, 31 May 2012 20:08:26 +0200
>  >>  From:schl...@uni-mainz.de
>  >>  To:gmx-users@gromacs.org
>  >>  Subject: [gmx-users] Re: boundaries in PMF
>  >>
>  >>  Where is the center of mass of reference group (MOL) located?
>  >>
>  >>  It seems that the COM is near the middle of the ion channel. Since 
you
>  >>  use 'pull_geometry=distance', g_wham will look only for the distance
>  >>  between 'MOL' and 'Na' and that leads to problem.
>  >>  If the com of 'MOL' sits in the center of the channel (which is 
around
>  >>  5nm long), one has 2.5nm in both directions. Since g_wham uses only 
the
>  >>  distance you get the PMF for half of the channel, but with the data 
of
>  >>  both parts.
>  >>  If the channel would be symmetric and the com of 'MOL' would lie 
exactly
>  >>  in the middle of the channel, this could be ok. But if even one of 
both
>  >>  assumptions is wrong, the results would be errorous.
>  >>
>  >>  A better approach would be to use 'pull_geometry=direction', since 
the
>  >>  you define a vector along which the windows lie and do not have the
>  >>  problem that the distance is in both directions (along positive and
>  >>  negative vector) the same.
>  >>  Only problem could be that g_wham supports 'pull_geometry=direction'
>  >>  only from gromacs 4.5.x (don't know this, since instead of umbrella
>  >>  smapling i use thermodynamik integration, where one uses constraints
>  >>  (instead of restraints) and integrates the constraint-force; but the
>  >>  conceptual problem with 'distance/direction' is the same).
>  >>
>  >>  Another approach (with 'pull_geometry=distance') would be to use a
>  >>  reference group which is just outside of the cha

[gmx-users] Results of the GROMACS user survey & NVIDIA board winners

[Erik Lindahl]

Hi,

First: Let me thank each and every one of you who took the trouble to fill out 
our user survey. The resulting information is invaluable to us, and Mark Berger 
of NVIDIA has been a tremendous help in assembling the results and statistics 
for us. This WILL affect future development, and we are currently preparing 
some information from it to put online - stay tuned.

However, there was also an incentive part to it ;-)

It gives me great pleasure to formally announce the two winners of C2075 cards 
generously donated by NVIDIA through Mark:

* Florian Dommert, Institute for Computational Physics, University Stuttgart
* Emmanuel Birru, Monash University, Parkville Campus


Big congratulations to both winners from the GROMACS & NVIDIA teams, and let me 
convey a *very* big and special thank-you to Mark Berger for making this 
possible! 

All the best,

Erik
--
Erik Lindahl 
Professor of Theoretical & Computational Biophysics, Royal Institute of 
Technology
Professor of Computational Structural Biology, Stockholm University
Tel:  +46855378029 (KTH) +468164675 (SU)


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[gmx-users] Configurational bias Monte Carlo

[Benjamin Haley]

Hello,

   I have found the excellent documentation for creating polymer
chains in GROMACS.  I want to create several chains and pack
them into a volume, adjusting torsion angles to minimize
interactions with other chains (and self-interaction within a chain).
One method for doing this is the configurational bias Monte Carlo
sampling.  Can this (or something similar) be done in GROMACS?

Thank you!
Ben Haley
Purdue University
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Re: [gmx-users] Configurational bias Monte Carlo

[Michael Shirts]

There's a fair amount of interest for more general support for Monte
Carlo methods in GROMACS 5.0.  However, there is no any current
support for configuration bias Monte Carlo (or any other kind of MC)
currently in the code.

On Fri, Jun 1, 2012 at 12:10 PM, Benjamin Haley  wrote:
> Hello,
>
>   I have found the excellent documentation for creating polymer
> chains in GROMACS.  I want to create several chains and pack
> them into a volume, adjusting torsion angles to minimize
> interactions with other chains (and self-interaction within a chain).
> One method for doing this is the configurational bias Monte Carlo
> sampling.  Can this (or something similar) be done in GROMACS?
>
> Thank you!
> Ben Haley
> Purdue University
> --
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Re: [gmx-users] Configurational bias Monte Carlo

[Lara Bunte]

Hi

>Monte Carlo methods in GROMACS 5.0. 


Thats cool, when will GROMACS 5.0 be released? 


Greetings
Lara






- Ursprüngliche Message -
Von: Michael Shirts 
An: Discussion list for GROMACS users 
CC: 
Gesendet: 18:24 Freitag, 1.Juni 2012
Betreff: Re: [gmx-users] Configurational bias Monte Carlo

There's a fair amount of interest for more general support for Monte
Carlo methods in GROMACS 5.0.  However, there is no any current
support for configuration bias Monte Carlo (or any other kind of MC)
currently in the code.

On Fri, Jun 1, 2012 at 12:10 PM, Benjamin Haley  wrote:
> Hello,
>
>   I have found the excellent documentation for creating polymer
> chains in GROMACS.  I want to create several chains and pack
> them into a volume, adjusting torsion angles to minimize
> interactions with other chains (and self-interaction within a chain).
> One method for doing this is the configurational bias Monte Carlo
> sampling.  Can this (or something similar) be done in GROMACS?
>
> Thank you!
> Ben Haley
> Purdue University
> --
> gmx-users mailing list    gmx-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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Re: [gmx-users] Configurational bias Monte Carlo

[Justin A. Lemkul]

On 6/1/12 12:28 PM, Lara Bunte wrote:

Hi


Monte Carlo methods in GROMACS 5.0.



Thats cool, when will GROMACS 5.0 be released?




There is no release date yet.  Version 4.6 is still coming together.

-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] Results of the GROMACS user survey & NVIDIA board winners

[Dommert Florian]

On Fri, 2012-06-01 at 18:09 +0200, Erik Lindahl wrote: 
> Hi,
> 
> First: Let me thank each and every one of you who took the trouble to fill 
> out our user survey. The resulting information is invaluable to us, and Mark 
> Berger of NVIDIA has been a tremendous help in assembling the results and 
> statistics for us. This WILL affect future development, and we are currently 
> preparing some information from it to put online - stay tuned.
> 
> However, there was also an incentive part to it ;-)
> 
> It gives me great pleasure to formally announce the two winners of C2075 
> cards generously donated by NVIDIA through Mark:
> 
> * Florian Dommert, Institute for Computational Physics, University Stuttgart
> * Emmanuel Birru, Monash University, Parkville Campus
> 
> 
> Big congratulations to both winners from the GROMACS & NVIDIA teams, and let 
> me convey a *very* big and special thank-you to Mark Berger for making this 
> possible! 
> 

Thank you very much for this generous gift. If I consider the tiny
amount of time required to complete the survey compared to the effort
you spent in the development of GROMACS it was the least I could do.

/Flo   


> All the best,
> 
> Erik
> --
> Erik Lindahl 
> Professor of Theoretical & Computational Biophysics, Royal Institute of 
> Technology
> Professor of Computational Structural Biology, Stockholm University
> Tel:  +46855378029 (KTH) +468164675 (SU)
> 
> 

-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658


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[gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface

[Christopher Neale]

Dear Hugh:


I can't answer your question, but I can address the error message that you see.

Basically, your semi-isotropic pressure coupling allows the surface area of the 
water-decane

interface to get smaller as z increases and x and y decrease. In a system with 
only water

and decane, this will continue until you have a single file of decane aligned 
in z.

To avoid this, you need to use semi-isotropic pressure coupling but set the 
compressibility

to zero in the z dimension (or, alternatively set the compressibility to zero 
in both x and y).

This will get rid of the error message, as I see that you have already noted.

So I guess that all I can tell you is that your first option is not going to be 
possible and

that your second option is giving you the wrong value because your surfactants 
are fighting the

elongation of your box along z, but the effect persists.


Chris.


-- original message --


Dear Gromacs users,

I have do simulation of surfactant at oil/water interface for a long time.
But I find it too difficult to get a reasonable interfacial tension. The
key question is the pcoupltype.

My system:

Box size:  3.0 * 3.0 * 13
> Molecule Number: decane 230, water 2041
> pcoupltype = semiisotropic

Gromacs version: 4.5.5


1. When I set compressibility = 4.5e-5 4.5e-5.  Surfactant number is 32
. The box will be shrink at x and y. At last simualion will end for a fatal
error:

One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.
For more information and tips for troubleshooting, please check the GROMACS.

2. When I add the number of surfactants to 40. compressibility = 4.5e-5
4.5e-5. The interfacial tension is -20bar/nm for two interfaces.  It is not
reasonable because it should be positive.

3. When I compressibility = 0 4.5e-5.  Surfactant number is 32. The
interfacial tension is 794bar/nm for two interfaces.


My question is:

What is the right way to simulate for this system?  My work confused me too
much.  Very appreciate for you help.

Hugh
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[gmx-users] unit conversion of a force constant

[Christopher Neale]

Your conversion is correct (Although you should use 1 cal=4.184 J (not 4.19)),
and yes, this is an absurdly strong force constant. I'm not sure what you mean 
by
a physically realisitic value though.

-- original message --


If I have a force constant 287 kcal/(mol * A^2), the A stands for Angstrom and 
I want to calculate this to kJ/(mol * nm^2), is it correct that I have to 
multiply 4.19/0.01 = 419 to the force constant?


Is ithis true:  287 kcal/(mol * A^2) = 120253 kJ/(mol * nm^2)

Could this be a physical realistic value or is this a hint, that 287 kcal/(mol 
* A^2) makes no sense for a force constant?

Thanks for helping
Greetings
Lara
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RE: [gmx-users] Results of the GROMACS user survey & NVIDIA board winners

[Emanuel Birru]

I would like to thank for your generous gift Mark (NVIDIA) and for all GROMACS 
team for the effort you made in developing the software and allowing us to use 
it for free and on top of that for your great support in solving our problem on 
this forum.  

As Florian mentioned, the time it takes to completing the survey and what you 
spent in the development of GROMACS is incomparable.

Cheers,
Emmanuel Birru

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Dommert Florian [domm...@icp.uni-stuttgart.de]
Sent: Saturday, June 02, 2012 3:05 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Results of the GROMACS user survey & NVIDIA board  
winners

On Fri, 2012-06-01 at 18:09 +0200, Erik Lindahl wrote:
> Hi,
>
> First: Let me thank each and every one of you who took the trouble to fill 
> out our user survey. The resulting information is invaluable to us, and Mark 
> Berger of NVIDIA has been a tremendous help in assembling the results and 
> statistics for us. This WILL affect future development, and we are currently 
> preparing some information from it to put online - stay tuned.
>
> However, there was also an incentive part to it ;-)
>
> It gives me great pleasure to formally announce the two winners of C2075 
> cards generously donated by NVIDIA through Mark:
>
> * Florian Dommert, Institute for Computational Physics, University Stuttgart
> * Emmanuel Birru, Monash University, Parkville Campus
>
>
> Big congratulations to both winners from the GROMACS & NVIDIA teams, and let 
> me convey a *very* big and special thank-you to Mark Berger for making this 
> possible!
>

Thank you very much for this generous gift. If I consider the tiny
amount of time required to complete the survey compared to the effort
you spent in the development of GROMACS it was the least I could do.

/Flo


> All the best,
>
> Erik
> --
> Erik Lindahl 
> Professor of Theoretical & Computational Biophysics, Royal Institute of 
> Technology
> Professor of Computational Structural Biology, Stockholm University
> Tel:  +46855378029 (KTH) +468164675 (SU)
>
>

--
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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[gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface

[Klniu]

Dear Chris:

Thank you for your help. Maybe I can try it as this. First set x and y
fixed by setting compressibility = 0 4.5e-0.5 until the system
reaching equilibrium and then release. If it sounds reasonable. I am
trying to do it.

Dear Hugh:

I can't answer your question, but I can address the error message that you see.

Basically, your semi-isotropic pressure coupling allows the surface
area of the water-decane

interface to get smaller as z increases and x and y decrease. In a
system with only water

and decane, this will continue until you have a single file of decane
aligned in z.

To avoid this, you need to use semi-isotropic pressure coupling but
set the compressibility

to zero in the z dimension (or, alternatively set the compressibility
to zero in both x and y).

This will get rid of the error message, as I see that you have already noted.

So I guess that all I can tell you is that your first option is not
going to be possible and

that your second option is giving you the wrong value because your
surfactants are fighting the

elongation of your box along z, but the effect persists.

Chris.

-- original message --

Dear Gromacs users,

I have do simulation of surfactant at oil/water interface for a long time.

But I find it too difficult to get a reasonable interfacial tension. The

key question is the pcoupltype.

My system:

Box size:  3.0 * 3.0 * 13

>* Molecule Number: decane 230, water 2041*

>* pcoupltype = semiisotropic*

Gromacs version: 4.5.5

1. When I set compressibility = 4.5e-5 4.5e-5.  Surfactant number is 32

. The box will be shrink at x and y. At last simualion will end for a fatal

error:

One of the box vectors has become shorter than twice the cut-off length or

box_yy-|box_zy| or box_zz has become smaller than the cut-off.

For more information and tips for troubleshooting, please check the GROMACS.

2. When I add the number of surfactants to 40. compressibility = 4.5e-5

4.5e-5. The interfacial tension is -20bar/nm for two interfaces.  It is not

reasonable because it should be positive.

3. When I compressibility = 0 4.5e-5.  Surfactant number is 32. The

interfacial tension is 794bar/nm for two interfaces.

My question is:

What is the right way to simulate for this system?  My work confused me too

much.  Very appreciate for you help.

Hugh
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[gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface

[Christopher Neale]

No, the point is that the equilibrium surface area is near zero in the context 
of PBC and you need

special tricks to keep the system away from that equilibrium.

There will always be a force toward reducing the surface area of the

hydrophobic/hydrophilic interface. It is possible to disallow this force to 
cause system

relaxation by using an incompressible Cartesian z (or x and y), but as soon as 
you let that go

the system will then relax toward the tall and thin column of aliphatic chains.

Perhaps you should return to the list with a detailed description of what

you are trying to accomplish and you might get some help. I doubt that I can 
help that part,

but there is likely somebody out there who can. Also, you will increase your 
chances of

getting help from somebody like me (expert gromacs user who is totally ignorant 
of your

particular field of study) by giving proper explanations of thing like the

"interfacial tension of surfactant at oil/water interface". I know that it 
makes sense to you

(and probably lots of other people), but I for one don't know exactly what you 
are trying to

accomplish.


Chris.



-- original message --

Dear Chris:

Thank you for your help. Maybe I can try it as this. First set x and y
fixed by setting compressibility = 0 4.5e-0.5 until the system
reaching equilibrium and then release. If it sounds reasonable. I am
trying to do it.

Dear Hugh:
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Re: [gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface

[Klniu]

Very thank you for your suggestion and being so kind. I will write a new
detailed subject and explain my purpose.

On Sat, Jun 2, 2012 at 10:23 AM, Christopher Neale <
chris.ne...@mail.utoronto.ca> wrote:

>  No, the point is that the equilibrium surface area is near zero in the 
> context of PBC and you need
>
> special tricks to keep the system away from that equilibrium.
>
> There will always be a force toward reducing the surface area of the
>
> hydrophobic/hydrophilic interface. It is possible to disallow this force to 
> cause system
>
> relaxation by using an incompressible Cartesian z (or x and y), but as soon 
> as you let that go
>
> the system will then relax toward the tall and thin column of aliphatic 
> chains.
>
> Perhaps you should return to the list with a detailed description of what
>
> you are trying to accomplish and you might get some help. I doubt that I can 
> help that part,
>
> but there is likely somebody out there who can. Also, you will increase your 
> chances of
>
> getting help from somebody like me (expert gromacs user who is totally 
> ignorant of your
>
> particular field of study) by giving proper explanations of thing like the
>
> "interfacial tension of surfactant at oil/water interface". I know that it 
> makes sense to you
>
> (and probably lots of other people), but I for one don't know exactly what 
> you are trying to
>
> accomplish.
>
>
> Chris.
>
>
>
> -- original message --
>
> Dear Chris:
>
> Thank you for your help. Maybe I can try it as this. First set x and y
> fixed by setting compressibility = 0 4.5e-0.5 until the system
> reaching equilibrium and then release. If it sounds reasonable. I am
> trying to do it.
>
> Dear Hugh:
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>
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[gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?

[Klniu]

Dear Gromacs users,

I am doing a membrane simulation. The system are two layers composed
by surfactants. other molecule are decane and water. The system like
this:

decane

---

surfactant
> ---

water
> ---

surfactant

---

decane

My research is to get the surface tension  between decane and water. I
mainly use NPT simulation to reach equilibrium and product.

when I set pcoupl = semiisotropic and compressibility  = 4.5e-5 4.5e-5, the
box at x and y will shrink incessantly and then the system crashes.

My question is:
1. Is my direction of work worng? There is another way to do this simution?
2. how can I get surface tension?

The content of mdp file is below:

> ; NEIGHBORSEARCHING PARAMETERS
>
> ; nblist update frequency
>
> nstlist  = 10
>
> ; ns algorithm (simple or grid)
>
> ns_type  = grid
>
> ; Periodic boundary conditions: xyz, no, xy
>
> pbc  = xyz
>
> periodic_molecules   = no
>
> ; nblist cut-off
>
> rlist= 1.0
>
> ; long-range cut-off for switched potentials
>
> rlistlong= -1
>
>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>
> ; Method for doing electrostatics
>
> coulombtype  = PME
>
> rcoulomb-switch  = 0
>
> rcoulomb = 1.0
>
> ; Relative dielectric constant for the medium and the reaction field
>
> epsilon_r= 1
>
> epsilon_rf   = 1
>
> ; Method for doing Van der Waals
>
> vdw-type = Cut-off
>
> ; cut-off lengths
>
> rvdw-switch  = 0
>
> rvdw = 1.4
>
> ; Apply long range dispersion corrections for Energy and Pressure
>
> dispcorr = EnerPres
>
> ; Extension of the potential lookup tables beyond the cut-off
>
> table-extension  = 1
>
> ; Seperate tables between energy group pairs
>
> energygrp_table  =
>
> ; Spacing for the PME/PPPM FFT grid
>
> fourierspacing   = 0.135
>
> ; FFT grid size, when a value is 0 fourierspacing will be used
>
> fourier_nx   = 0
>
> fourier_ny   = 0
>
> fourier_nz   = 0
>
> ; EWALD/PME/PPPM parameters
>
> pme_order= 4
>
> ewald_rtol   = 1e-05
>
> ewald_geometry   = 3d
>
> epsilon_surface  = 0
>
> optimize_fft = yes
>
>
>> ; IMPLICIT SOLVENT ALGORITHM
>
> implicit_solvent = No
>
>
>> ; GENERALIZED BORN ELECTROSTATICS
>
> ; Algorithm for calculating Born radii
>
> gb_algorithm = Still
>
> ; Frequency of calculating the Born radii inside rlist
>
> nstgbradii   = 1
>
> ; Cutoff for Born radii calculation; the contribution from atoms
>
> ; between rlist and rgbradii is updated every nstlist steps
>
> rgbradii = 1
>
> ; Dielectric coefficient of the implicit solvent
>
> gb_epsilon_solvent   = 80
>
> ; Salt concentration in M for Generalized Born models
>
> gb_saltconc  = 0
>
> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
>
> gb_obc_alpha = 1
>
> gb_obc_beta  = 0.8
>
> gb_obc_gamma = 4.85
>
> gb_dielectric_offset = 0.009
>
> sa_algorithm = Ace-approximation
>
> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
>
> ; The value -1 will set default value for Still/HCT/OBC GB-models.
>
> sa_surface_tension   = -1
>
>
>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>
> ; Temperature coupling
>
> tcoupl   = Nose-Hoover
>
> nsttcouple   = -1
>
> nh-chain-length  = 10
>
> ; Groups to couple separately
>
> tc-grps  = OIL DRG SOL
>
> ; Time constant (ps) and reference temperature (K)
>
> tau_t= 0.5 0.5 0.5
>
> ref_t= 300 300 300
>
> ; Pressure coupling
>
> pcoupl   = Parrinello-Rahman
>
> pcoupltype   = semiisotropic
>
> nstpcouple   = -1
>
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
>
> tau_p= 2.0 2.0
>
> compressibility  = 4.5e-5 4.5e-5
>
> ref_p= 1.0 1.0
>
>
I have post a mail in list but my description is not clear.
http://lists.gromacs.org/pipermail/gmx-users/2012-June/072000.html

Thank you.

Hugh.
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Re: [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?

[Mark Abraham]

On 2/06/2012 1:11 PM, Klniu wrote:

Dear Gromacs users,
I am doing a membrane simulation. The system are two layers composed by 
surfactants. other molecule are decane and water. The system like this:

decane 

--- 


surfactant
--- 


water
--- 

surfactant 

--- 


decane

My research is to get the surface tension  between decane and water. I 
mainly use NPT simulation to reach equilibrium and product.


when I set pcoupl = semiisotropic and compressibility  = 4.5e-5 
4.5e-5, the box at x and y will shrink incessantly and then the system 
crashes.


My question is:
1. Is my direction of work worng? There is another way to do this 
simution?

2. how can I get surface tension?


Equilibration with P-R pressure coupling is asking for trouble. Use 
Berendsen to get close, then switch. Otherwise, see 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up


Mark



The content of mdp file is below:

; NEIGHBORSEARCHING PARAMETERS

; nblist update frequency

nstlist  = 10

; ns algorithm (simple or grid)

ns_type  = grid

; Periodic boundary conditions: xyz, no, xy

pbc  = xyz

periodic_molecules   = no

; nblist cut-off 


rlist= 1.0

; long-range cut-off for switched potentials

rlistlong= -1


; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype  = PME

rcoulomb-switch  = 0

rcoulomb = 1.0

; Relative dielectric constant for the medium and the reaction
field

epsilon_r= 1

epsilon_rf   = 1

; Method for doing Van der Waals

vdw-type = Cut-off

; cut-off lengths 


rvdw-switch  = 0

rvdw = 1.4

; Apply long range dispersion corrections for Energy and Pressure

dispcorr = EnerPres

; Extension of the potential lookup tables beyond the cut-off

table-extension  = 1

; Seperate tables between energy group pairs

energygrp_table  = 


; Spacing for the PME/PPPM FFT grid

fourierspacing   = 0.135

; FFT grid size, when a value is 0 fourierspacing will be used

fourier_nx   = 0

fourier_ny   = 0

fourier_nz   = 0

; EWALD/PME/PPPM parameters

pme_order= 4

ewald_rtol   = 1e-05

ewald_geometry   = 3d

epsilon_surface  = 0

optimize_fft = yes


; IMPLICIT SOLVENT ALGORITHM

implicit_solvent = No


; GENERALIZED BORN ELECTROSTATICS

; Algorithm for calculating Born radii

gb_algorithm = Still

; Frequency of calculating the Born radii inside rlist

nstgbradii   = 1

; Cutoff for Born radii calculation; the contribution from atoms

; between rlist and rgbradii is updated every nstlist steps

rgbradii = 1

; Dielectric coefficient of the implicit solvent

gb_epsilon_solvent   = 80

; Salt concentration in M for Generalized Born models

gb_saltconc  = 0

; Scaling factors used in the OBC GB model. Default values are
OBC(II)

gb_obc_alpha = 1

gb_obc_beta  = 0.8

gb_obc_gamma = 4.85

gb_dielectric_offset = 0.009

sa_algorithm = Ace-approximation

; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface)
part of GBSA

; The value -1 will set default value for Still/HCT/OBC GB-models.

sa_surface_tension   = -1


; OPTIONS FOR WEAK COUPLING ALGORITHMS

; Temperature coupling 


tcoupl   = Nose-Hoover

nsttcouple   = -1

nh-chain-length  = 10

; Groups to couple separately

tc-grps  = OIL DRG SOL

; Time constant (ps) and reference temperature (K)

tau_t= 0.5 0.5 0.5

ref_t= 300 300 300

; Pressure coupling 


pcoupl   = Parrinello-Rahman

pcoupltype   = semiisotropic

nstpcouple   = -1

; Time constant (ps), compressibility (1/bar) and reference P
(bar)

tau_p= 2.0 2.0

compressibility  = 4.5e-5 4.5e-5

ref_p= 1.0 1.0

I have post a mail in list but my description is not clear. 
http:/

Re: [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?

[Klniu]

Sorry for my carelessness. Before nose-hoover, Parrinello-Rahman, I have
done v-rescale, berendsen already. tau_t = 0.1, tau_p = 0.5.

Hugh.

On Sat, Jun 2, 2012 at 12:43 PM, Mark Abraham wrote:

>  On 2/06/2012 1:11 PM, Klniu wrote:
>
> Dear Gromacs users,
>
> I am doing a membrane simulation. The system are two layers composed by 
> surfactants. other molecule are decane and water. The system like this:
>
> decane
>
> ---
>
> surfactant
>> ---
>
> water
>> ---
>
> surfactant
>
> ---
>
> decane
>
> My research is to get the surface tension  between decane and water. I
> mainly use NPT simulation to reach equilibrium and product.
>
>  when I set pcoupl = semiisotropic and compressibility  = 4.5e-5 4.5e-5,
> the box at x and y will shrink incessantly and then the system crashes.
>
>  My question is:
> 1. Is my direction of work worng? There is another way to do this simution?
> 2. how can I get surface tension?
>
>
> Equilibration with P-R pressure coupling is asking for trouble. Use
> Berendsen to get close, then switch. Otherwise, see
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> Mark
>
>
>
>  The content of mdp file is below:
>
>> ; NEIGHBORSEARCHING PARAMETERS
>>
>> ; nblist update frequency
>>
>> nstlist  = 10
>>
>> ; ns algorithm (simple or grid)
>>
>> ns_type  = grid
>>
>> ; Periodic boundary conditions: xyz, no, xy
>>
>> pbc  = xyz
>>
>> periodic_molecules   = no
>>
>> ; nblist cut-off
>>
>> rlist= 1.0
>>
>> ; long-range cut-off for switched potentials
>>
>> rlistlong= -1
>>
>>
>>>  ; OPTIONS FOR ELECTROSTATICS AND VDW
>>
>> ; Method for doing electrostatics
>>
>> coulombtype  = PME
>>
>> rcoulomb-switch  = 0
>>
>> rcoulomb = 1.0
>>
>> ; Relative dielectric constant for the medium and the reaction field
>>
>> epsilon_r= 1
>>
>> epsilon_rf   = 1
>>
>> ; Method for doing Van der Waals
>>
>> vdw-type = Cut-off
>>
>> ; cut-off lengths
>>
>> rvdw-switch  = 0
>>
>> rvdw = 1.4
>>
>> ; Apply long range dispersion corrections for Energy and Pressure
>>
>> dispcorr = EnerPres
>>
>> ; Extension of the potential lookup tables beyond the cut-off
>>
>> table-extension  = 1
>>
>> ; Seperate tables between energy group pairs
>>
>> energygrp_table  =
>>
>> ; Spacing for the PME/PPPM FFT grid
>>
>> fourierspacing   = 0.135
>>
>> ; FFT grid size, when a value is 0 fourierspacing will be used
>>
>> fourier_nx   = 0
>>
>> fourier_ny   = 0
>>
>> fourier_nz   = 0
>>
>> ; EWALD/PME/PPPM parameters
>>
>> pme_order= 4
>>
>> ewald_rtol   = 1e-05
>>
>> ewald_geometry   = 3d
>>
>> epsilon_surface  = 0
>>
>> optimize_fft = yes
>>
>>
>>>  ; IMPLICIT SOLVENT ALGORITHM
>>
>> implicit_solvent = No
>>
>>
>>>  ; GENERALIZED BORN ELECTROSTATICS
>>
>> ; Algorithm for calculating Born radii
>>
>> gb_algorithm = Still
>>
>> ; Frequency of calculating the Born radii inside rlist
>>
>> nstgbradii   = 1
>>
>> ; Cutoff for Born radii calculation; the contribution from atoms
>>
>> ; between rlist and rgbradii is updated every nstlist steps
>>
>> rgbradii = 1
>>
>> ; Dielectric coefficient of the implicit solvent
>>
>> gb_epsilon_solvent   = 80
>>
>> ; Salt concentration in M for Generalized Born models
>>
>> gb_saltconc  = 0
>>
>> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
>>
>> gb_obc_alpha = 1
>>
>> gb_obc_beta  = 0.8
>>
>> gb_obc_gamma = 4.85
>>
>> gb_dielectric_offset = 0.009
>>
>> sa_algorithm = Ace-approximation
>>
>> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
>>
>> ; The value -1 will set default value for Still/HCT/OBC GB-models.
>>
>> sa_surface_tension   = -1
>>
>>
>>>  ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>>
>> ; Temperature coupling
>>
>> tcoupl   = Nose-Hoover
>>
>> nsttcouple   = -1
>>
>> nh-chain-length  = 10
>>
>> ; Groups to couple separately
>>
>> tc-grps  = OIL DRG SOL
>>
>> ; Time constant (ps) and reference temperature (K)
>>
>> tau_t= 0.5 0.5 0.5
>>
>> ref_t= 300 300 300
>>
>> ; Pressure coupling
>>
>> pcoupl   = Parrinello-Rahman
>>
>> pcoupltype   = semiisotropic
>>
>> nstpcouple   = -1
>>
>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
>>
>> tau_p= 2.0 2.0
>>
>> compressibility  = 4.5e-5 4.5e-5
>>
>> ref_p= 1.0 1.0
>>
>>
> I have post a mail in list but my description is not clear.
> http://lists.gromacs.org/pipermail/gmx-users/2012-June/072000.