Re: [gmx-users] Installing/Uninstalling

[Nikhil Maroli]

You can Install without uninstalling in different path,
-DCMAKE_INSTALL_PREFIX=xxx
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[gmx-users] radius of gyration in REMD of protein

[YanhuaOuyang]

Hi,
   I am running a REMD of a protein,  which ranged from 270 to 500K in explicit 
water model with 60 replicas,  and I stop to analyse the REMD data after 
running for 50ns. I use the demux.pl script to get the continue the coordinate 
for each replica. Then I calculate the Rg value for each replica. However, the 
Rg fluctuation of each replica differs dramatically, some fluctuate 
dramatically, some converge well. Do someone knows the reason, or the 
fluctuation is normal ? How can I check my REMD is running correctlly?
the commad of Rg calculation is below:
gmx gyrate -s md_0_0.tpr   -f   *_continue_trajectory_pbc_mol.xtc  -o 
gyrate_*.xvg

Best regards,
Ouyang
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Re: [gmx-users] Problem compiling on Bluegene/Q

[Jernej Zidar]

Dear Mark,

Thanks for the explanation.

Best,
Jernej

On Thu, Aug 18, 2016 at 8:22 PM  Sorry, there's a typo in how we named that file. I've fixed it for 5.1.4,
> but you need to use
>
> -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-bgclang-cxx
>
> for now.
>
> < snip >

>
> XL compilers on BlueGene are no longer supported in 2016, for exactly this
> reason. I've updated the future install guide to be explicit about this.
>
> Mark
>
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Re: [gmx-users] Gromacs 2016 building issue

[Victor Rosas Garcia]

I thought the "build" directory had to be *outside* the gromacs source
directory.  Don't know for sure if that makes a difference.

2016-08-18 18:20 GMT-05:00 Quentin Kaas :

> Hi Mark,
>
> Thank you for your answer. I just have redone again everything but I get
> the same problem. I am not even compiling with MPI or GPU support and I
> have the same.
>
> Hereis my procedure:
> """
> tar xzvf gromacs-2016.tar.gz
> cd gromacs-2016
> mkdir build
> cd build/
> cmake -DGMX_GPU=OFF -DGMX_MPI=OFF -DCMAKE_INSTALL_PREFIX=/home/
> q.kaas/share/gromacs-2016_nompi/ -DGMX_BUILD_OWN_FFTW=ON
> -DBUILD_SHARED_LIBS=OFF -DGMX_SIMD=AVX_256 ..
> nice -20 make -j 2
> """
>
> And the answer is the same:
>
> """
> (...)
> [100%] Built target libgromacs
> Linking CXX executable ../../bin/template
> /opt/pkg/2015Q2/lib/libxml2.so.2: undefined reference to `gzopen64'
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error
> """
>
> What is this "template" doing? Could that be coming from this binary?
> There is no such thing in 5.1.3.
>
> Thank you
> Quentin
>
>
>
> On 18/08/16 22:17, Mark Abraham wrote:
>
> Hi,
>
> GROMACS 2016 doesn't use libxml2 at all, so it looks like there's something
> strange going on with how you've done that build, because there's no way
> the template can have such a linking dependency.
>
> Mark
>
> On Thu, Aug 18, 2016 at 2:43 AM Quentin Kaas  
>  wrote:
>
>
> Hello,
>
> I just tried building Gromacs2016. The build went fine until it reached
> the linking stage:
>
> linking CXX executable ../../bin/template
> /opt/pkg/2015Q2/lib/libxml2.so.2: undefined reference to `gzopen64'
> collect2: error: ld returned 1 exit status
> make[1]: *** [bin/template] Error 1
> make: *** [share/template/CMakeFiles/template.dir/all] Error 2
>
> Could someone help me tell cmake to tell ld where the zlib library is?
>
> I compiled Gromacs-5.1.3 about 10 min before trying the new 2016 version
> and it went without any complaint. There might be something to fix in the
> 2016 version?
>
> Best wishes
>
> Quentin
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>
>
> --
> *Dr Quentin Kaas*
>
> Institute for Molecular Bioscience (IMB)
> Level 2 North, Building 80, The University of Queensland, Brisbane QLD
> 4072, Australia
> F: +61 7 3346 2021
>
> http://researchers.uq.edu.au/researcher/1804
> http://www.conoserver.org/
> http://cybase.org.au/
>
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Re: [gmx-users] Gromacs 2016 building issue

[Quentin Kaas]

  
  
Hi Mark,
Thank you for your answer. I just have redone again everything
  but I get the same problem. I am not even compiling with MPI or
  GPU support and I have the same.
Hereis my procedure:
"""
tar xzvf gromacs-2016.tar.gz
cd gromacs-2016
mkdir build
cd build/
cmake -DGMX_GPU=OFF -DGMX_MPI=OFF
-DCMAKE_INSTALL_PREFIX=/home/q.kaas/share/gromacs-2016_nompi/
-DGMX_BUILD_OWN_FFTW=ON -DBUILD_SHARED_LIBS=OFF -DGMX_SIMD=AVX_256
..
nice -20 make -j 2
"""

And the answer is the same:

"""
(...)
[100%] Built target libgromacs
Linking CXX executable ../../bin/template
/opt/pkg/2015Q2/lib/libxml2.so.2: undefined reference to `gzopen64'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 
"""

What is this "template" doing? Could that be coming from this
binary? There is no such thing in 5.1.3.

Thank you
Quentin



On 18/08/16 22:17, Mark Abraham wrote:


  Hi,

GROMACS 2016 doesn't use libxml2 at all, so it looks like there's something
strange going on with how you've done that build, because there's no way
the template can have such a linking dependency.

Mark

On Thu, Aug 18, 2016 at 2:43 AM Quentin Kaas  wrote:


  
Hello,

I just tried building Gromacs2016. The build went fine until it reached
the linking stage:

linking CXX executable ../../bin/template
/opt/pkg/2015Q2/lib/libxml2.so.2: undefined reference to `gzopen64'
collect2: error: ld returned 1 exit status
make[1]: *** [bin/template] Error 1
make: *** [share/template/CMakeFiles/template.dir/all] Error 2

Could someone help me tell cmake to tell ld where the zlib library is?

I compiled Gromacs-5.1.3 about 10 min before trying the new 2016 version
and it went without any complaint. There might be something to fix in the
2016 version?

Best wishes

Quentin
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send a mail to gmx-users-requ...@gromacs.org.

  


-- 
  
Dr Quentin Kaas

Institute for Molecular Bioscience (IMB)

  Level 2 North, Building 80, The University of Queensland,
  Brisbane QLD 4072, Australia
  F: +61 7 3346 2021



  http://researchers.uq.edu.au/researcher/1804
  http://www.conoserver.org/
  http://cybase.org.au/

  

  

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[gmx-users] Installing/Uninstalling

[Steve Seibold]

HelloI have Gromacs 4.5.4 installed (without the MPI enabled for multiple 
machines) on a Fedora 18 OS; but would like to install Gromacs 5.0.4 with MPI 
enabled. I want to run REMD simulations and it is my understandingthat I need 
MPI enabled (even for a quad-core machine) to run separated simulations on 
different threads. I have OpenMPI version 1.6.3 on my Fedora 18 machine. I am 
using this machine as a pre-run to set up systems to run on a large cluster. I 
am assuming that I need to uninstall Gromacs 4.5.4; but am not sure how to do 
this. I attempted to locate “how to” in the gromacs web site but could not find 
it and I looked in the manual.  I ran “Which mdrun” and found two locations. 
One was /usr/local/bin which has ftww hard lincs and gromacs symbolic lincs to 
the other directory at /usr/local/gromacs. I am assuming to uninstall I would 
remove/usr/local/gromacs…correct? Thanks, Steve
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[gmx-users] GROMACS performance :installation

[Nikhil Maroli]

Dear all,
We have following  workstations

2 x 12 core processor + 3 x GTX 980 Ti
2 x 12 core processor + 3 x GTX 1070
2 x 8 core processor + 2 xGTX 1070 and Tesla K20

and a Desktop system with Single  i7 processor (8 core) + GTX 1070

Previously I installed with flag DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda(8 core System with tesla k20)

i used to run single job;
 gmx mdrun -nt X -deffnm XX -gpu_id 0

can I proceed with the same installation set for the above systems? or
should I compile with CUDA+MPI? or any other options?

I planned to run at least two Gromacs jobs in one workstation ,Which will
give the best performance.?




-- 
Regards,
Nikhil Maroli
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Re: [gmx-users] Diffusion coefficient water

[Victor Rosas Garcia]

The following paper may also be interesting.

"System-size corrections for self-diffusion coefficients calculated from
molecular dynamics simulations: The case of CO2, n-alkanes, and
poly(ethylene glycol) dimethyl ether" J. Chem. Phys. 145, 074109 (2016);
http://dx.doi.org/10.1063/1.4960776


2016-08-18 8:35 GMT-05:00 Michael Shirts :

> See the following paper
> (http://pubs.acs.org/doi/abs/10.1021/ct400109a) for some examples of
> diffusion calculations in GROMACS.
>
> The finite size correction for diffusion coefficients is something
> different than the long range energy corrections. A discussion of this
> (I can't vouch for all the details, I just googled) is here:
> http://pubs.acs.org/doi/abs/10.1021/jp0756247
>
>
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Re: [gmx-users] Problem with binding energy

[Ben Tam]

Hi Justin,


Yes I am, doing 3 single point simulation but using a very long winded way of 
doing single - point energy. The DFT calculation gave me -357 kJ/mol, the other 
software I mentioned is Forcite, which gave me around -250 kJ/mol.


Ben



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: 18 August 2016 13:21
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem with binding energy



On 8/18/16 8:13 AM, Ben Tam wrote:
> Hi Billy,
>
>
> To be more exact, the system has been energy minimised through DFT 
> calculation. We want to compare that with MM force field by using the same 
> co-ordinate.  Henceforth we don't need an average gibbs energy but one 
> specific frame energy calculation.
>

You're doing the single-point energy correctly, right?

http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
Single-Point Energy - 
Gromacs
www.gromacs.org
Computing the energy of a single configuration is an operation that is 
sometimes useful. The best way to do this with GROMACS is with the mdrun -rerun 
mechanism ...




It's not clear to me from the description whether you are or not.

The -250 kJ/mol is the interaction energy from DFT, I presume?

-Justin

> Best regards,
>
> Ben
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Billy 
> Williams-Noonan 
> Sent: 18 August 2016 13:07
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problem with binding energy
>
> Hi Ben,
>
>My understanding of what you've done is that you have calculated a
> binding enthalpy for the water at a specific, non-biological temperature,
> and not a Gibbs free energy that you would expect from experiment...
>
> Billy
>
> On 18 August 2016 at 21:34, Ben Tam  wrote:
>
>> Dear all,
>>
>>
>> I have a problem with calculation with binding energy with using gromacs.
>> My calculation is the binding of solvent onto a crystal.
>>
>>
>> The steps I took to calculate binding energy is like this:
>>
>>
>> 1) Energy minimised my crystal system with the solvent.
>>
>>
>> 2) Calculated the energy of the crystal-solvent system by using gmx energy
>> - total energy is selected (this is done by using only time 0 energy step
>> shown from energy.xvg)
>>
>>
>> 3) I extract the co-ordinate of the solvent from the minimised system and
>> calculate the energy by using gmx energy - total energy is selected (this
>> is done by using only time step 0 energy shown from energy.xvg)
>>
>>
>> 4)Extract the co-ordinate of the crystal from the minimised system and
>> calculate the energy similar to the previous step.
>>
>>
>> 5) Energy of the Crystalsolvent system - energy of the crystal - energy of
>> the solvent = binding energy.
>>
>>
>> The problem I have is, after the calculation I proposed, the binding shown
>> as -6000 kJ/mol. With other software, the binding energy is calculated  as
>> -250 kJ/mol.
>>
>> I have triple check my molecules connectivity and the charges and the
>> force field. Everything seems to be reasonable. Henceforth, what can caused
>> the extremely high binding energy?
>>
>>
>> Thanks ,
>>
>>
>> Ben
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
> Gromacs - Gromacs
> www.gromacs.org
> The development of Gromacs would not have been possible without generous 
> funding support from the European Research Council, the Swedish Research 
> Council, the Swedish ...
>
>
>
>> Support/Mailing_Lists/GMX-Users_List before posting!
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>>
>
>
>
> --
> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
> 
> **|*   +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, 

Re: [gmx-users] Diffusion coefficient water

[Michael Shirts]

See the following paper
(http://pubs.acs.org/doi/abs/10.1021/ct400109a) for some examples of
diffusion calculations in GROMACS.

The finite size correction for diffusion coefficients is something
different than the long range energy corrections. A discussion of this
(I can't vouch for all the details, I just googled) is here:
http://pubs.acs.org/doi/abs/10.1021/jp0756247

On Thu, Aug 18, 2016 at 6:37 AM, Mark Abraham  wrote:
> Hi,
>
> I would also consider using a pressure-coupling algorithm that isn't known
> to create the wrong velocity distribution.
>
> Mark
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Re: [gmx-users] Diffusion coefficient water

[Mark Abraham]

Hi,

I would also consider using a pressure-coupling algorithm that isn't known
to create the wrong velocity distribution.

Mark
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Re: [gmx-users] Diffusion coefficient water

[Justin Lemkul]

On 8/18/16 6:48 AM, Diez Fernandez, Amanda wrote:

Thanks Justin and Nikhil,

1) So in principle is it expected that results will be different and I
should take my final value to be the average of, say, 10 simulations?



Yes, averaging over multiple, independent simulations is the correct approach.


2)If so, the average over my simulations is not similar to the published
average. They also use a unit cell of 216 molecules (I use 221 molecules).
They have "long-range corrections for both the energy and pressure². Is
this equivalent to DispCorr= EnerPres ? What other
corrections should I do?



DispCorr = EnerPres is correct.  If you're having trouble reproducing a 
published result, you should ask the authors of the study for their advice.


-Justin


Thanks,
Amanda




On 17/08/2016, 19:28, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
 wrote:


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Today's Topics:

  1. Re: Diffusion coefficient water (Nikhil Maroli)
  2. Re: Diffusion coefficient water (Justin Lemkul)
  3. is there martini CG parameters for K+ ion? (li he)
  4. Re: Diffusion coefficient water (li he)
  5. Fwd: is there martini CG parameters for K+ ion? (li he)
  6. Re: Diffusion coefficient water (li he)


--

Message: 1
Date: Wed, 17 Aug 2016 21:49:45 +0530
From: Nikhil Maroli 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Diffusion coefficient water
Message-ID:

Re: [gmx-users] Problem with binding energy

[Billy Williams-Noonan]

Apologies those were negative values.

On 18 August 2016 at 22:21, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

> So gromacs gives an answer of 6000 kJ/mol and some other software using
> the same method yields 250 kJ/mol ?
>
> On 18 August 2016 at 22:13, Ben Tam  wrote:
>
>> Hi Billy,
>>
>>
>> To be more exact, the system has been energy minimised through DFT
>> calculation. We want to compare that with MM force field by using the same
>> co-ordinate.  Henceforth we don't need an average gibbs energy but one
>> specific frame energy calculation.
>>
>> Best regards,
>>
>> Ben
>>
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Billy
>> Williams-Noonan 
>> Sent: 18 August 2016 13:07
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Problem with binding energy
>>
>> Hi Ben,
>>
>>My understanding of what you've done is that you have calculated a
>> binding enthalpy for the water at a specific, non-biological temperature,
>> and not a Gibbs free energy that you would expect from experiment...
>>
>> Billy
>>
>> On 18 August 2016 at 21:34, Ben Tam  wrote:
>>
>> > Dear all,
>> >
>> >
>> > I have a problem with calculation with binding energy with using
>> gromacs.
>> > My calculation is the binding of solvent onto a crystal.
>> >
>> >
>> > The steps I took to calculate binding energy is like this:
>> >
>> >
>> > 1) Energy minimised my crystal system with the solvent.
>> >
>> >
>> > 2) Calculated the energy of the crystal-solvent system by using gmx
>> energy
>> > - total energy is selected (this is done by using only time 0 energy
>> step
>> > shown from energy.xvg)
>> >
>> >
>> > 3) I extract the co-ordinate of the solvent from the minimised system
>> and
>> > calculate the energy by using gmx energy - total energy is selected
>> (this
>> > is done by using only time step 0 energy shown from energy.xvg)
>> >
>> >
>> > 4)Extract the co-ordinate of the crystal from the minimised system and
>> > calculate the energy similar to the previous step.
>> >
>> >
>> > 5) Energy of the Crystalsolvent system - energy of the crystal - energy
>> of
>> > the solvent = binding energy.
>> >
>> >
>> > The problem I have is, after the calculation I proposed, the binding
>> shown
>> > as -6000 kJ/mol. With other software, the binding energy is calculated
>> as
>> > -250 kJ/mol.
>> >
>> > I have triple check my molecules connectivity and the charges and the
>> > force field. Everything seems to be reasonable. Henceforth, what can
>> caused
>> > the extremely high binding energy?
>> >
>> >
>> > Thanks ,
>> >
>> >
>> > Ben
>> >
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/
>> Gromacs - Gromacs
>> www.gromacs.org
>> The development of Gromacs would not have been possible without generous
>> funding support from the European Research Council, the Swedish Research
>> Council, the Swedish ...
>>
>>
>>
>> > Support/Mailing_Lists/GMX-Users_List before posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>>
>>
>>
>> --
>> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>>
>> *LinkedIn Profile
>> > prof-0-sb-preview-primary-button>
>> **|*   +61420 382 557
>>
>> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
>> Royal Parade, Parkville, 3052
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
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>> send a mail to gmx-users-requ...@gromacs.org.
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>
>
>
> --
> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
> 
> **|*   +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
>
>


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*LinkedIn Profile

Re: [gmx-users] Problem with binding energy

[Justin Lemkul]

On 8/18/16 8:13 AM, Ben Tam wrote:

Hi Billy,


To be more exact, the system has been energy minimised through DFT calculation. 
We want to compare that with MM force field by using the same co-ordinate.  
Henceforth we don't need an average gibbs energy but one specific frame energy 
calculation.



You're doing the single-point energy correctly, right?

http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

It's not clear to me from the description whether you are or not.

The -250 kJ/mol is the interaction energy from DFT, I presume?

-Justin


Best regards,

Ben


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Billy 
Williams-Noonan 
Sent: 18 August 2016 13:07
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem with binding energy

Hi Ben,

   My understanding of what you've done is that you have calculated a
binding enthalpy for the water at a specific, non-biological temperature,
and not a Gibbs free energy that you would expect from experiment...

Billy

On 18 August 2016 at 21:34, Ben Tam  wrote:


Dear all,


I have a problem with calculation with binding energy with using gromacs.
My calculation is the binding of solvent onto a crystal.


The steps I took to calculate binding energy is like this:


1) Energy minimised my crystal system with the solvent.


2) Calculated the energy of the crystal-solvent system by using gmx energy
- total energy is selected (this is done by using only time 0 energy step
shown from energy.xvg)


3) I extract the co-ordinate of the solvent from the minimised system and
calculate the energy by using gmx energy - total energy is selected (this
is done by using only time step 0 energy shown from energy.xvg)


4)Extract the co-ordinate of the crystal from the minimised system and
calculate the energy similar to the previous step.


5) Energy of the Crystalsolvent system - energy of the crystal - energy of
the solvent = binding energy.


The problem I have is, after the calculation I proposed, the binding shown
as -6000 kJ/mol. With other software, the binding energy is calculated  as
-250 kJ/mol.

I have triple check my molecules connectivity and the charges and the
force field. Everything seems to be reasonable. Henceforth, what can caused
the extremely high binding energy?


Thanks ,


Ben

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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Problem compiling on Bluegene/Q

[Mark Abraham]

Hi,


On Thu, Aug 11, 2016 at 9:05 AM Jernej Zidar  wrote:

> Hi guys,
>   I am trying to compile Gromacs 2016 for a Bluegene/Q machine and I've
> encountered a small error during the cmake/configure stage:
>
> [ihpczidj@cumulus gromacs-build]$ rm -rf * && cmake ../gromacs-2016
> -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-bgclang-CXX -DGMX_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/home/ihpczidj/scratch/ -DGMX_BUILD_OWN_FFTW=ON
> -DGMX_BUILD_MDRUN_ONLY=ON
> -DCMAKE_C_COMPILER=/bgsys/drivers/ppcfloor/comm/xl/bin/mpicc
> -DCMAKE_CXX_COMPILER=/bgsys/drivers/ppcfloor/comm/xl/bin/mpicxx
>
> CMake Error at
> /home/ihpczidj/scratch/cmake-2.8.10.2/share/cmake-2.8/
> Modules/CMakeDetermineSystem.cmake:95
> (message):
>
>   Could not find toolchain file: Platform/BlueGeneQ-static-bgclang-CXX
>

Sorry, there's a typo in how we named that file. I've fixed it for 5.1.4,
but you need to use

-DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-bgclang-cxx

for now.


> Call Stack (most recent call first):
>
>   CMakeLists.txt:45 (project)
>
>
>
> CMake Error: Error required internal CMake variable not set, cmake may be
> not be built correctly.
>
> Missing variable is:
>
> CMAKE_C_COMPILER_ENV_VAR
>
> CMake Error: Could not find cmake module
> file:/home/ihpczidj/scratch/gromacs-build/CMakeFiles/
> 2.8.10.2/CMakeCCompiler.cmake
>
> CMake Error: Error required internal CMake variable not set, cmake may be
> not be built correctly.
>
> Missing variable is:
>
> CMAKE_CXX_COMPILER_ENV_VAR
>
> CMake Error: Could not find cmake module
> file:/home/ihpczidj/scratch/gromacs-build/CMakeFiles/
> 2.8.10.2/CMakeCXXCompiler.cmake
>
> -- Configuring incomplete, errors occurred!
>
> [ihpczidj@cumulus gromacs-build]$ rm -rf * && cmake ../gromacs-2016
> -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C -DGMX_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/home/ihpczidj/scratch/ -DGMX_BUILD_OWN_FFTW=ON
> -DGMX_BUILD_MDRUN_ONLY=ON
> -DCMAKE_C_COMPILER=/bgsys/drivers/ppcfloor/comm/xl/bin/mpicc
> -DCMAKE_CXX_COMPILER=/bgsys/drivers/ppcfloor/comm/xl/bin/mpicxx
>
> -- The C compiler identification is XL 12.1.0
>
> -- The CXX compiler identification is XL 12.1.0
>
> -- Check for working C compiler: /bgsys/drivers/ppcfloor/comm/xl/bin/mpicc
>
> -- Check for working C compiler: /bgsys/drivers/ppcfloor/comm/xl/bin/mpicc
> -- works
>
> -- Detecting C compiler ABI info
>
> -- Detecting C compiler ABI info - done
>
> -- Check for working CXX compiler:
> /bgsys/drivers/ppcfloor/comm/xl/bin/mpicxx
>
> -- Check for working CXX compiler:
> /bgsys/drivers/ppcfloor/comm/xl/bin/mpicxx -- works
>
> -- Detecting CXX compiler ABI info
>
> -- Detecting CXX compiler ABI info - done
>
> -- Performing Test CXXFLAG_STD_CXX0X
>
> -- Performing Test CXXFLAG_STD_CXX0X - Failed
>
> -- Performing Test CXX11_SUPPORTED
>
> -- Performing Test CXX11_SUPPORTED - Failed
>
> CMake Error at cmake/gmxTestCXX11.cmake:113 (message):
>
>   This version of GROMACS requires a C++11 compiler.  Please use a newer
>
>   compiler or use the GROMACS 5.1.x release.  See the installation guide
> for
>
>   details.
>

XL compilers on BlueGene are no longer supported in 2016, for exactly this
reason. I've updated the future install guide to be explicit about this.

Mark


> Call Stack (most recent call first):
>
>   CMakeLists.txt:164 (gmx_test_cxx11)
>
>
>  Before doing the cmake I set the various variables by doing this:
>
> export PATH=/bgsys/drivers/ppcfloor/comm/xl/bin/:$PATH
>
> export
> LD_LIBRARY_PATH=/bgsys/drivers/ppcfloor/comm/xl/lib/:$LD_LIBRARY_PATH
>
> export CXX=/bgsys/drivers/ppcfloor/comm/xl/bin/mpicxx
>
> export CC=/bgsys/drivers/ppcfloor/comm/xl/bin/mpicc
>
>
>   Gromacs 5.1.3 compiles without a problem.
>
>   Can you advise what could be wrong? As you can see I tried to use the
> recommended plaftorm settings for 2016 and the old ones.
>
>
> Thanks in advance,
>
> Jernej
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Problem with binding energy

[Billy Williams-Noonan]

So gromacs gives an answer of 6000 kJ/mol and some other software using the
same method yields 250 kJ/mol ?

On 18 August 2016 at 22:13, Ben Tam  wrote:

> Hi Billy,
>
>
> To be more exact, the system has been energy minimised through DFT
> calculation. We want to compare that with MM force field by using the same
> co-ordinate.  Henceforth we don't need an average gibbs energy but one
> specific frame energy calculation.
>
> Best regards,
>
> Ben
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Billy
> Williams-Noonan 
> Sent: 18 August 2016 13:07
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problem with binding energy
>
> Hi Ben,
>
>My understanding of what you've done is that you have calculated a
> binding enthalpy for the water at a specific, non-biological temperature,
> and not a Gibbs free energy that you would expect from experiment...
>
> Billy
>
> On 18 August 2016 at 21:34, Ben Tam  wrote:
>
> > Dear all,
> >
> >
> > I have a problem with calculation with binding energy with using gromacs.
> > My calculation is the binding of solvent onto a crystal.
> >
> >
> > The steps I took to calculate binding energy is like this:
> >
> >
> > 1) Energy minimised my crystal system with the solvent.
> >
> >
> > 2) Calculated the energy of the crystal-solvent system by using gmx
> energy
> > - total energy is selected (this is done by using only time 0 energy step
> > shown from energy.xvg)
> >
> >
> > 3) I extract the co-ordinate of the solvent from the minimised system and
> > calculate the energy by using gmx energy - total energy is selected (this
> > is done by using only time step 0 energy shown from energy.xvg)
> >
> >
> > 4)Extract the co-ordinate of the crystal from the minimised system and
> > calculate the energy similar to the previous step.
> >
> >
> > 5) Energy of the Crystalsolvent system - energy of the crystal - energy
> of
> > the solvent = binding energy.
> >
> >
> > The problem I have is, after the calculation I proposed, the binding
> shown
> > as -6000 kJ/mol. With other software, the binding energy is calculated
> as
> > -250 kJ/mol.
> >
> > I have triple check my molecules connectivity and the charges and the
> > force field. Everything seems to be reasonable. Henceforth, what can
> caused
> > the extremely high binding energy?
> >
> >
> > Thanks ,
> >
> >
> > Ben
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> Gromacs - Gromacs
> www.gromacs.org
> The development of Gromacs would not have been possible without generous
> funding support from the European Research Council, the Swedish Research
> Council, the Swedish ...
>
>
>
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
>  trk=prof-0-sb-preview-primary-button>
> **|*   +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
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>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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Re: [gmx-users] Gromacs 2016 building issue

[Mark Abraham]

Hi,

GROMACS 2016 doesn't use libxml2 at all, so it looks like there's something
strange going on with how you've done that build, because there's no way
the template can have such a linking dependency.

Mark

On Thu, Aug 18, 2016 at 2:43 AM Quentin Kaas  wrote:

> Hello,
>
> I just tried building Gromacs2016. The build went fine until it reached
> the linking stage:
>
> linking CXX executable ../../bin/template
> /opt/pkg/2015Q2/lib/libxml2.so.2: undefined reference to `gzopen64'
> collect2: error: ld returned 1 exit status
> make[1]: *** [bin/template] Error 1
> make: *** [share/template/CMakeFiles/template.dir/all] Error 2
>
> Could someone help me tell cmake to tell ld where the zlib library is?
>
> I compiled Gromacs-5.1.3 about 10 min before trying the new 2016 version
> and it went without any complaint. There might be something to fix in the
> 2016 version?
>
> Best wishes
>
> Quentin
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] CPU running doesn't match command line

[Mark Abraham]

Hi,

It's a bit curious to want to run two 8-thread jobs on a machine with 10
physical cores because you'll get lots of performance imbalance because
some threads must share the same physical core, but I guess it's a free
world. As I suggested the other day,
http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html#examples-for-mdrun-on-one-node
has
some examples. The fact you've compiled and linked with an MPI library
means it may be involving itself in the thread-affinity management, but
whether it is doing that is something between you, it, the docs and the
cluster admins. If you're just wanting to run on a single node, do yourself
a favour and build the thread-MPI flavour.

If so, you probably want more like
gmx mdrun -ntomp 10 -pin on -pinoffset 0 -gpu_id 0 -s run1
gmx mdrun -ntomp 10 -pin on -pinoffset 10 -gpu_id 1 -s run2

If you want to use the MPI build, then I suggest you read up on how its
mpirun will let you manage keeping the threads of processes where you want
them (ie apart).

Mark

On Thu, Aug 18, 2016 at 7:57 AM Albert  wrote:

> anybody has more suggestions?
>
> thx a lot
>
>
> On 08/17/2016 09:07 AM, Albert wrote:
> > Hello:
> >
> > Here is the information that you asked for.
> >
> >   gmx_mpi mdrun -s 7.tpr -v -g 7.log -c 7.gro -x 7.xtc -ntomp 8
> > -gpu_id 0 -pin on
> >
> 
> >
> > GROMACS:  gmx mdrun, VERSION 5.1.3
> > Executable:   /soft/gromacs/5.1.3_intel/bin/gmx_mpi
> > Data prefix:  /soft/gromacs/5.1.3_intel
> > Command line:
> >   gmx_mpi mdrun -s 7.tpr -v -g 7.log -c 7.gro -x 7.xtc -ntomp 8
> > -gpu_id 0 -pin on
> >
> > GROMACS version:VERSION 5.1.3
> > Precision:  single
> > Memory model:   64 bit
> > MPI library:MPI
> > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
> > GPU support:enabled
> > OpenCL support: disabled
> > invsqrt routine:gmx_software_invsqrt(x)
> > SIMD instructions:  AVX_256
> > FFT library:fftw-3.3.4-sse2
> > RDTSCP usage:   enabled
> > C++11 compilation:  disabled
> > TNG support:enabled
> > Tracing support:disabled
> > Built on:   Thu Aug 11 16:15:26 CEST 2016
> > Built by:   albert@cudaB [CMAKE]
> > Build OS/arch:  Linux 3.16.7-35-desktop x86_64
> > Build CPU vendor:   GenuineIntel
> > Build CPU brand:Intel(R) Xeon(R) CPU E5-2690 v2 @ 3.00GHz
> > Build CPU family:   6   Model: 62   Stepping: 4
> > Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm
> > mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp
> > sse2 sse3 sse4.1
> > sse4.2 ssse3 tdt x2apic
> > C compiler: /soft/intel/impi/5.1.3.223/bin64/mpicc GNU 4.8.3
> > C compiler flags:-mavx-Wextra -Wno-missing-field-initializers
> > -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value
> > -Wunused-parameter  -
> > O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds
> > C++ compiler:   /soft/intel/impi/5.1.3.223/bin64/mpicxx GNU 4.8.3
> > C++ compiler flags:  -mavx-Wextra -Wno-missing-field-initializers
> > -Wpointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG
> > -funroll-all-loops -fexcess-pre
> > cision=fast  -Wno-array-bounds
> > Boost version:  1.54.0 (external)
> > CUDA compiler:  /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda
> > compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on
> > Wed_May__4_21:01:56_CDT
> > _2016;Cuda compilation tools, release 8.0, V8.0.26
> > CUDA compiler
> >
> flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=
> >
> sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode
> >
> >
> ;arch=compute_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;;
> > ;-mavx;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wal
> >
> l;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
> >
> > CUDA driver:8.0
> > CUDA runtime:   8.0
> >
> > Running on 1 node with total 10 cores, 20 logical cores, 2 compatible
> > GPUs
> > Hardware detected on host cudaB (the node of MPI rank 0):
> >   CPU info:
> > Vendor: GenuineIntel
> > Brand:  Intel(R) Xeon(R) CPU E5-2690 v2 @ 3.00GHz
> > Family:  6  model: 62  stepping:  4
> > CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm
> > mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp
> > sse2 sse3 sse4.1 ss
> > e4.2 ssse3 tdt x2apic
> > SIMD instructions most likely to fit this hardware: AVX_256
> > SIMD instructions selected at GROMACS compile time: AVX_256
> >   GPU info:
> > 

Re: [gmx-users] Problem with binding energy

[Ben Tam]

Hi Billy,


To be more exact, the system has been energy minimised through DFT calculation. 
We want to compare that with MM force field by using the same co-ordinate.  
Henceforth we don't need an average gibbs energy but one specific frame energy 
calculation.

Best regards,

Ben


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Billy 
Williams-Noonan 
Sent: 18 August 2016 13:07
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem with binding energy

Hi Ben,

   My understanding of what you've done is that you have calculated a
binding enthalpy for the water at a specific, non-biological temperature,
and not a Gibbs free energy that you would expect from experiment...

Billy

On 18 August 2016 at 21:34, Ben Tam  wrote:

> Dear all,
>
>
> I have a problem with calculation with binding energy with using gromacs.
> My calculation is the binding of solvent onto a crystal.
>
>
> The steps I took to calculate binding energy is like this:
>
>
> 1) Energy minimised my crystal system with the solvent.
>
>
> 2) Calculated the energy of the crystal-solvent system by using gmx energy
> - total energy is selected (this is done by using only time 0 energy step
> shown from energy.xvg)
>
>
> 3) I extract the co-ordinate of the solvent from the minimised system and
> calculate the energy by using gmx energy - total energy is selected (this
> is done by using only time step 0 energy shown from energy.xvg)
>
>
> 4)Extract the co-ordinate of the crystal from the minimised system and
> calculate the energy similar to the previous step.
>
>
> 5) Energy of the Crystalsolvent system - energy of the crystal - energy of
> the solvent = binding energy.
>
>
> The problem I have is, after the calculation I proposed, the binding shown
> as -6000 kJ/mol. With other software, the binding energy is calculated  as
> -250 kJ/mol.
>
> I have triple check my molecules connectivity and the charges and the
> force field. Everything seems to be reasonable. Henceforth, what can caused
> the extremely high binding energy?
>
>
> Thanks ,
>
>
> Ben
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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--
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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Re: [gmx-users] Problem with binding energy

[Billy Williams-Noonan]

Hi Ben,

   My understanding of what you've done is that you have calculated a
binding enthalpy for the water at a specific, non-biological temperature,
and not a Gibbs free energy that you would expect from experiment...

Billy

On 18 August 2016 at 21:34, Ben Tam  wrote:

> Dear all,
>
>
> I have a problem with calculation with binding energy with using gromacs.
> My calculation is the binding of solvent onto a crystal.
>
>
> The steps I took to calculate binding energy is like this:
>
>
> 1) Energy minimised my crystal system with the solvent.
>
>
> 2) Calculated the energy of the crystal-solvent system by using gmx energy
> - total energy is selected (this is done by using only time 0 energy step
> shown from energy.xvg)
>
>
> 3) I extract the co-ordinate of the solvent from the minimised system and
> calculate the energy by using gmx energy - total energy is selected (this
> is done by using only time step 0 energy shown from energy.xvg)
>
>
> 4)Extract the co-ordinate of the crystal from the minimised system and
> calculate the energy similar to the previous step.
>
>
> 5) Energy of the Crystalsolvent system - energy of the crystal - energy of
> the solvent = binding energy.
>
>
> The problem I have is, after the calculation I proposed, the binding shown
> as -6000 kJ/mol. With other software, the binding energy is calculated  as
> -250 kJ/mol.
>
> I have triple check my molecules connectivity and the charges and the
> force field. Everything seems to be reasonable. Henceforth, what can caused
> the extremely high binding energy?
>
>
> Thanks ,
>
>
> Ben
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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[gmx-users] Problem with binding energy

[Ben Tam]

Dear all,


I have a problem with calculation with binding energy with using gromacs. My 
calculation is the binding of solvent onto a crystal.


The steps I took to calculate binding energy is like this:


1) Energy minimised my crystal system with the solvent.


2) Calculated the energy of the crystal-solvent system by using gmx energy - 
total energy is selected (this is done by using only time 0 energy step shown 
from energy.xvg)


3) I extract the co-ordinate of the solvent from the minimised system and 
calculate the energy by using gmx energy - total energy is selected (this is 
done by using only time step 0 energy shown from energy.xvg)


4)Extract the co-ordinate of the crystal from the minimised system and 
calculate the energy similar to the previous step.


5) Energy of the Crystalsolvent system - energy of the crystal - energy of the 
solvent = binding energy.


The problem I have is, after the calculation I proposed, the binding shown as 
-6000 kJ/mol. With other software, the binding energy is calculated  as -250 
kJ/mol.

I have triple check my molecules connectivity and the charges and the force 
field. Everything seems to be reasonable. Henceforth, what can caused the 
extremely high binding energy?


Thanks ,


Ben

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Re: [gmx-users] Fwd: is there martini CG parameters for K+ ion?

[Peter Kroon]

Hi,


disturbing to hear you can't register on our forums. We've been having
some trouble with the website, so we'll definitely look into it.

As for the science: Na+ and K+ are identical in Martini. The size
difference is compensated by the implicit solvation shell anyway. You'd
have to look into the literature to find a validation for this though, I
don't have it handy.


Good luck,

Peter


On 17-08-16 20:26, li he wrote:
> Dear gmxers,
> I am not sure if I'd better post my question here, but the martini forum
> http://www.cgmartini.nl/index.php/forum  does not allow me register and
> post my
> question there.
> I am trying to simulate some KCl solution, but only find martini CG Na+
> parameters
> at http://cgmartini.nl/images/parameters/ITP/martini_v2.0_ions.itp
> I am wondering where I can find martini parameters for K+ ion, or can I
> just use martini
> Na+ parameters for K+?
> If there is a martini parameter of K+, I could image it should be Qd bead
> with +1 charge, exactly the same as Na+ parameters at the above link. Yes,
> it is upsetting to use the same parameter for Na+ and K+, but we have to
> admit the current martini force field is not very fine tuned, thus have to
> just use Na+ martini parameters at the above link for K+ if we want to
> simulate CG KCl or martini KCl anyway? Can this way be justified if the
> simulation results agree with the results of other studies, either
> experiments or simulations?
> Thanks a lot for your kind help, and any suggestion or comment is very
> welcome.
> Yours
> he li


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Re: [gmx-users] Diffusion coefficient water

[Diez Fernandez, Amanda]

Thanks Justin and Nikhil,

1) So in principle is it expected that results will be different and I
should take my final value to be the average of, say, 10 simulations?

2)If so, the average over my simulations is not similar to the published
average. They also use a unit cell of 216 molecules (I use 221 molecules).
They have "long-range corrections for both the energy and pressure². Is
this equivalent to DispCorr= EnerPres ? What other
corrections should I do?

Thanks,
Amanda
 
 


On 17/08/2016, 19:28, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
 wrote:

>Send gromacs.org_gmx-users mailing list submissions to
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>
>Today's Topics:
>
>   1. Re: Diffusion coefficient water (Nikhil Maroli)
>   2. Re: Diffusion coefficient water (Justin Lemkul)
>   3. is there martini CG parameters for K+ ion? (li he)
>   4. Re: Diffusion coefficient water (li he)
>   5. Fwd: is there martini CG parameters for K+ ion? (li he)
>   6. Re: Diffusion coefficient water (li he)
>
>
>--
>
>Message: 1
>Date: Wed, 17 Aug 2016 21:49:45 +0530
>From: Nikhil Maroli 
>To: gromacs.org_gmx-users@maillist.sys.kth.se
>Subject: Re: [gmx-users] Diffusion coefficient water
>Message-ID:
>   

[gmx-users] MM/PBSA for protein-membrane system

[Nikhil Maroli]

What is the possibility of using MM/PBSA method for calculating interaction
energy between Protein and membrane?

-- 
Regards,
Nikhil Maroli
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