Re: [gmx-users] Gibbs free energy of binding

[mohsen ramezanpour]

Dear Justin

If I do  two  MD simulations for a short time in the same conditions(of
course separately for protein and drug)
 and calculate total energy of each one and sum them with each other as E1
as nonbonding free energy of system.
then a MD simulation for Protein-drug system in the same condition and
calculate it's total energy too as E2 as bound system .
what does (E1-E2)mean?
I think it is binding free energy,Is not it?
in the other hand when we are working on NPT ensamble it means Gibbs free
energy is the main energy and our total energy is equal to Gibbs free
energy.
Then,what is the problem?





On Wed, Oct 20, 2010 at 3:31 PM, Justin A. Lemkul  wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear Justin
>> You are right,But I searched in tools and I found g_sham
>> It is very useful tool for estimating Gibbs free energy,Enthalepy ,
>> emtropy and ...
>> I think I can use from that for my calculation of binding free energy(In
>> the other words,del G free energy of system )
>> how do you think about g_sham?
>>
>>
>>
> It is not applicable.  g_sham simply determines free energies based on
> histograms of two independent variables.  PMF is the appropriate technique
> for what you want to do.  I can see no other effective way to conduct your
> study using Gromacs.
>
> -Justin
>
>
>> On Wed, Oct 20, 2010 at 2:28 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>mohsen ramezanpour wrote:
>>
>>Dear Gromacs users
>>
>>I want to calculate Gibbs free energy too,but about Protein-drug
>>binding.
>>Please guide more clearly,what texts I need to read for learning
>>how can I do it?
>>
>>
>>Look into the literature and nearly any of the popular simulation
>>textbooks.
>>
>>
>>Besides,g-energy has an option for estimating free energy from
>>trajectory file(-fee option)
>>I thought if I had a trajectory file of binding state I could
>>estimate binding free energy by this option.
>>am  I right?
>>does it give me Gibbs free energy?(Is this equall to binding
>>free energy?)
>>
>>
>>Never used this option, but from the description of the option, it
>>calculates delta(G) relative to an ideal gas state, which sounds
>>completely unrelated to what you want to accomplish.
>>
>>Besides, if g_energy could magically solve this difficult problem,
>>no one would bother with more thorough methods, like PMF or
>>thermodynamic integration.
>>
>>-Justin
>>
>>thanks in advance
>>Mohsen
>>
>>
>>On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   shahab shariati wrote:
>>
>>   Hi gromacs users
>>Can I use gromacs for obtaining Gibbs free energy of
>>binding of
>>   protein and dna?
>>
>>
>>   Yes.  I would suggest you read about potential of mean force
>>   calculations.
>>
>>   -Justin
>>
>>   -- 
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   MILES-IGERT Trainee
>>   Department of Biochemistry
>>   Virginia Tech
>>   Blacksburg, VA
>>   jalemkul[at]vt.edu   | (540)
>>
>>231-9080
>>
>>   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>   
>>   -- gmx-users mailing listgmx-users@gromacs.org
>>
>>   >
>>
>>
>>   http://lists.gromacs.org/mailman/listinfo/gmx-users
>>   Please search the archive at
>>   http://www.gromacs.org/Support/Mailing_Lists/Search before
>>posting!
>>   Please don't post (un)subscribe requests to the list. Use the
>> www
>>   interface or send it to gmx-users-requ...@gromacs.org
>>
>>   >>.
>>
>>   Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at
>>http://www.gromacs.org/Support/Mailing

Re: [gmx-users] Gibbs free energy of binding

[Sander Pronk]

Hi Mohsen,

The mean energy difference is only one component of the free energy difference. 

Before you go any further I'd suggest reading a good book on molecular 
simulations, like 'Understanding Molecular Simulations' by Frenkel and Smit. 

There's a good reason free energy calculations cover over half of that book.

Sander


On Oct 21, 2010, at 09:18 , mohsen ramezanpour wrote:

> Dear Justin
> 
> If I do  two  MD simulations for a short time in the same conditions(of 
> course separately for protein and drug)
>  and calculate total energy of each one and sum them with each other as E1 as 
> nonbonding free energy of system.
> then a MD simulation for Protein-drug system in the same condition and 
> calculate it's total energy too as E2 as bound system .
> what does (E1-E2)mean?
> I think it is binding free energy,Is not it?
> in the other hand when we are working on NPT ensamble it means Gibbs free 
> energy is the main energy and our total energy is equal to Gibbs free energy.
> Then,what is the problem?
> 
> 
> 
> 
> 
> On Wed, Oct 20, 2010 at 3:31 PM, Justin A. Lemkul  wrote:
> 
> 
> mohsen ramezanpour wrote:
> Dear Justin
> You are right,But I searched in tools and I found g_sham
> It is very useful tool for estimating Gibbs free energy,Enthalepy ,
> emtropy and ...
> I think I can use from that for my calculation of binding free energy(In the 
> other words,del G free energy of system )
> how do you think about g_sham?
> 
> 
> 
> It is not applicable.  g_sham simply determines free energies based on 
> histograms of two independent variables.  PMF is the appropriate technique 
> for what you want to do.  I can see no other effective way to conduct your 
> study using Gromacs.
> 
> -Justin
> 
> 
> On Wed, Oct 20, 2010 at 2:28 PM, Justin A. Lemkul  > wrote:
> 
> 
> 
>mohsen ramezanpour wrote:
> 
>Dear Gromacs users
> 
>I want to calculate Gibbs free energy too,but about Protein-drug
>binding.
>Please guide more clearly,what texts I need to read for learning
>how can I do it?
> 
> 
>Look into the literature and nearly any of the popular simulation
>textbooks.
> 
> 
>Besides,g-energy has an option for estimating free energy from
>trajectory file(-fee option)
>I thought if I had a trajectory file of binding state I could
>estimate binding free energy by this option.
>am  I right?
>does it give me Gibbs free energy?(Is this equall to binding
>free energy?)
> 
> 
>Never used this option, but from the description of the option, it
>calculates delta(G) relative to an ideal gas state, which sounds
>completely unrelated to what you want to accomplish.
> 
>Besides, if g_energy could magically solve this difficult problem,
>no one would bother with more thorough methods, like PMF or
>thermodynamic integration.
> 
>-Justin
> 
>thanks in advance
>Mohsen
> 
> 
>On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul
>mailto:jalem...@vt.edu>
>>> wrote:
> 
> 
> 
>   shahab shariati wrote:
> 
>   Hi gromacs users
>Can I use gromacs for obtaining Gibbs free energy of
>binding of
>   protein and dna?
> 
> 
>   Yes.  I would suggest you read about potential of mean force
>   calculations.
> 
>   -Justin
> 
>   -- 
> 
>   Justin A. Lemkul
>   Ph.D. Candidate
>   ICTAS Doctoral Scholar
>   MILES-IGERT Trainee
>   Department of Biochemistry
>   Virginia Tech
>   Blacksburg, VA
>   jalemkul[at]vt.edu   | (540)
> 
>231-9080
> 
>   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>   
>   -- gmx-users mailing listgmx-users@gromacs.org
>
>   >
> 
> 
>   http://lists.gromacs.org/mailman/listinfo/gmx-users
>   Please search the archive at
>   http://www.gromacs.org/Support/Mailing_Lists/Search before
>posting!
>   Please don't post (un)subscribe requests to the list. Use the www
>   interface or send it to gmx-users-requ...@gromacs.org
>
>   >.
> 
>   Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 
>-- 
> 
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>MILES-IGERT Trainee
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu  | (

Re: [gmx-users] g_dipole ? => salt molecule in water => what is the the displacement vector pointing from the negative charge to the positive charge?

[Timo M.D. Graen]

reconsider your statement about the displacement vector. You should try 
to understand the concepts of vectors and reference points first. It is 
absolutely mandatory to do so before calculating dipole moments of 
charged systems. It might also be wise to use a small test system to 
practice on. For example take two ions for a start, Na+ and Cl-, place 
them at NA(1,1,0) and CL(2,1,0). Now calculate the dipole moment for 
this system using different points of reference, i.e. (0,0,0) and 
(1,2,0) and (3,3,0). What do you observe? Next, add an additional NA+ 
ion to your system at NA(3,1,0) and repeat your calculation for the same 
reference points. What do you observe now? Also compare your results to 
g_dipole for both systems. Are the results different in both cases? Now 
think about the difficulties for calculating dipole moments for charged 
molecules. The wikipedia sources you provided earlier should include all 
information necessary to calculate the answers to this problem.


On 10/21/2010 12:35 AM, Chih-Ying Lin wrote:



Hi
molecule dipole is 48.0 sum of q_i x_i

based on the following two websites,
/*x_i */ is the displacement vector
 pointing from
the negative charge to the positive charge.

what about the x_i for the salt-molecule, which dissociates into one
counter ion and the rest of the molecule in water?


http://en.wikipedia.org/wiki/Bond_dipole_moment
http://en.wikipedia.org/wiki/Electric_dipole_moment


Thank you
Lin



On 2010-10-20 06.06, Chih-Ying Lin wrote:
 >
 >
 >
 >
 > Hi
 > molecule dipole is 48.0 sum of q_i x_i
 > x_i the bond length for covalent bond.

No. x_i is the atomic position.

 > but what is "x_i" for salt-molecule?
 >
 >
 > For salt-molecule, the ionic bonds are broken in water solvent and the
 > counter ions are spread among the water.
 >
 > What is the "x_i" of the ionic bond in the dipole moment calculation?
 > Is x_i equal to the distance of the two parts of the salt-molecules (the
 > counter ion and the rest of the molecule) even though the salt molecule
 > has dissolved in the water?
 >
 > I mean, is x_i equal to the length of simulation box if the counter ion
 > and the rest of the molecule are in the two sides of the simulation box?
 >
 >
 > I mean, if Gromacs takes x_i as the length of simulation box if the
 > counter ion and the rest of the molecule are in the two sides of the
 > simulation box?
 >
 > Thank you
 > Lin
 >
 >
 >
 >
 >
 >
 >
 >
 >
 >
 > Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want
 > to read the part about calculating dipole moments for an array of point
 > charges, it is not difficult. 33 point charges are doable using pencil
 > and calculator in about 10min. Do not worry about the reference point as
 > long as your system is neutral, just set it to (0,0,0). Otherwise, take
 > any kind of first year physics book it will contain very similar
 > information.
 >
 > On 10/19/2010 05:39 AM, Chih-Ying Lin wrote:
 >>
 >>
 >>  Hi
 >>  According to the following website,
 >>
 >> http://en.wikipedia.org/wiki/Bond_dipole_moment
 >>
 >>
 >>  \mu = \delta \, d.
 >>  The bond dipole is modeled as +ä -- ä- with a distance /d/ between the
 >>  partial charges  +ä
and ä-.
 >>  For a complete molecule the total molecular dipole moment may be
 >>  approximated as the vector sum of individual bond dipole moments.
 >>
 >>
 >>  However, for a molecule of multiple atoms,
 >>  There may be more than one bond connected on one atom.
 >>  E
 >>  |
 >>  B - A - C
 >>  partial charge of atom_A = -0.5
 >>  partial charge of atom_B = 0.2
 >>  partial charge of atom_C = 0.35
 >>  partial charge of atom_E = 0.4
 >>
 >>
 >>
 >>  Which partial charges should I use when I calculate bond-dipole-moment
 >>  of A-B ?
 >>  Which partial charges should I use when I calculate bond-dipole-moment
 >>  of A-C ?
 >>  Which partial charges should I use when I calculate bond-dipole-moment
 >>  of A-E ?
 >>
 >>  Thank you
 >>  Lin
 >>
 >>
 >>
 >>
 >>
 >>
 >>
 >>  On 2010-10-18 03.30, Chih-Ying Lin wrote:
 >> >  HI
 >> >  I confined one molecule in the center of box and issue the g_dipole
 >>  command.
 >> >  The average dipole moment is still around 32.
 >> >  It is the molecule with 33 atoms / united atoms of most carbon
groups,
 >> >  isn't the dipole moment around 32 too high?
 >> >  How can I test next and know that the dipole moment around 32 is
 >> >  acceptable?
 >>  By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore
if you
 >>  have large charge separation you will get a large dipole.
 >>
 >> >  Thank you
 >> >  Lin
 >> >  On 2010-10-16 21.36, Chih-Ying Lin wrote:
 >> > >
 >> > > Hi
 >> > > I issue the g_dipole command on Gromacs => And, the following
 >> > > information is shown.
 >> > > There are 10 molecules in the selection,
 >> > > Does the Average =32.1611 refer to the average for a single over the
 >> > > simulation time?
 >> > > Or, th

[gmx-users] RE: Gibbs free energy of binding

[Ehud Schreiber]

Actually, I believe that using the energy difference, Delta E, as an
approximation to the free energy difference, Delta G, is a valid
approach (which I'm considering myself). The entropic contribution to
Delta G, namely -T Delta S, may be less prominent than Delta E.
In addition, Delta S can be approximated by various means - see e.g.
Doig & Sternberg 1995. I understand that such an approach is utilized in
the Accelrys Discovery Studio.
Obviously, this is an approximation that might be too crude for some
applications.

What do you think?


--

On Oct 21, 2010, at 09:25 , Sander Pronk wrote:

Hi Mohsen,

The mean energy difference is only one component of the free energy
difference. 

Before you go any further I'd suggest reading a good book on molecular
simulations, like 'Understanding Molecular Simulations' by Frenkel and
Smit. 

There's a good reason free energy calculations cover over half of that
book.

Sander


On Oct 21, 2010, at 09:18 , mohsen ramezanpour wrote:

> Dear Justin
> 
> If I do  two  MD simulations for a short time in the same
conditions(of course separately for protein and drug)
>  and calculate total energy of each one and sum them with each other
as E1 as nonbonding free energy of system.
> then a MD simulation for Protein-drug system in the same condition and
calculate it's total energy too as E2 as bound system .
> what does (E1-E2)mean?
> I think it is binding free energy,Is not it?
> in the other hand when we are working on NPT ensamble it means Gibbs
free energy is the main energy and our total energy is equal to Gibbs
free energy.
> Then,what is the problem?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] RE: Gibbs free energy of binding

[David van der Spoel]

On 2010-10-21 10.39, Ehud Schreiber wrote:

Actually, I believe that using the energy difference, Delta E, as an
approximation to the free energy difference, Delta G, is a valid
approach (which I'm considering myself). The entropic contribution to
Delta G, namely -T Delta S, may be less prominent than Delta E.
In addition, Delta S can be approximated by various means - see e.g.
Doig&  Sternberg 1995. I understand that such an approach is utilized in
the Accelrys Discovery Studio.
Obviously, this is an approximation that might be too crude for some
applications.


As a simple example the hydrophobic effect at room temperature is 
largely due to the entropy of the water [ at high temp it is due to the 
enthalpy of the water ].


Since the hydrophobic effect is involved in all ligand binding it seems 
quite hopeless to get any reliable numbers when neglecting entropy. No 
referee will buy that - I wouldn't.




What do you think?


--

On Oct 21, 2010, at 09:25 , Sander Pronk wrote:

Hi Mohsen,

The mean energy difference is only one component of the free energy
difference.

Before you go any further I'd suggest reading a good book on molecular
simulations, like 'Understanding Molecular Simulations' by Frenkel and
Smit.

There's a good reason free energy calculations cover over half of that
book.

Sander


On Oct 21, 2010, at 09:18 , mohsen ramezanpour wrote:


Dear Justin

If I do  two  MD simulations for a short time in the same

conditions(of course separately for protein and drug)

  and calculate total energy of each one and sum them with each other

as E1 as nonbonding free energy of system.

then a MD simulation for Protein-drug system in the same condition and

calculate it's total energy too as E2 as bound system .

what does (E1-E2)mean?
I think it is binding free energy,Is not it?
in the other hand when we are working on NPT ensamble it means Gibbs

free energy is the main energy and our total energy is equal to Gibbs
free energy.

Then,what is the problem?



--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Re: [gmx-users] RE: Gibbs free energy of binding

[Sander Pronk]

To put some numbers to what David said, here's an experimental paper on a 
well-studied drug-protein complex:
http://pubs.acs.org/doi/pdf/10.1021/bi001013s

the entropic contribution of HIV-1 protease inhibitor binding is about 3x 
bigger than the enthalpic contribution for all 4 drugs studied there. 

I'm not sure if that's a special case, but if you're leaving out entropy you 
are at the very least doing an uncontrolled approximation - you don't know how 
big the term is you're missing, and it could be the dominant term.

Sander


On 21 Oct 2010, at 10:45 , David van der Spoel wrote:

> On 2010-10-21 10.39, Ehud Schreiber wrote:
>> Actually, I believe that using the energy difference, Delta E, as an
>> approximation to the free energy difference, Delta G, is a valid
>> approach (which I'm considering myself). The entropic contribution to
>> Delta G, namely -T Delta S, may be less prominent than Delta E.
>> In addition, Delta S can be approximated by various means - see e.g.
>> Doig&  Sternberg 1995. I understand that such an approach is utilized in
>> the Accelrys Discovery Studio.
>> Obviously, this is an approximation that might be too crude for some
>> applications.
> 
> As a simple example the hydrophobic effect at room temperature is largely due 
> to the entropy of the water [ at high temp it is due to the enthalpy of the 
> water ].
> 
> Since the hydrophobic effect is involved in all ligand binding it seems quite 
> hopeless to get any reliable numbers when neglecting entropy. No referee will 
> buy that - I wouldn't.
> 
>> 
>> What do you think?
>> 
>> 
>> --
>> 
>> On Oct 21, 2010, at 09:25 , Sander Pronk wrote:
>> 
>> Hi Mohsen,
>> 
>> The mean energy difference is only one component of the free energy
>> difference.
>> 
>> Before you go any further I'd suggest reading a good book on molecular
>> simulations, like 'Understanding Molecular Simulations' by Frenkel and
>> Smit.
>> 
>> There's a good reason free energy calculations cover over half of that
>> book.
>> 
>> Sander
>> 
>> 
>> On Oct 21, 2010, at 09:18 , mohsen ramezanpour wrote:
>> 
>>> Dear Justin
>>> 
>>> If I do  two  MD simulations for a short time in the same
>> conditions(of course separately for protein and drug)
>>>  and calculate total energy of each one and sum them with each other
>> as E1 as nonbonding free energy of system.
>>> then a MD simulation for Protein-drug system in the same condition and
>> calculate it's total energy too as E2 as bound system .
>>> what does (E1-E2)mean?
>>> I think it is binding free energy,Is not it?
>>> in the other hand when we are working on NPT ensamble it means Gibbs
>> free energy is the main energy and our total energy is equal to Gibbs
>> free energy.
>>> Then,what is the problem?
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface 
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--
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Please search the archive at 
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[gmx-users] RE: Gibbs free energy of binding

[Ran Friedman]

Hi,

Under constant pressure a potential energy change is in many cases a good 
approximation for the change of enthalpy (if only small variations of volume 
are present). However, for many biomolecular applications, and in particular 
ligand binding, the entropy contribution cannot be neglected unless you compare 
two very similar reactions (e.g., delta delta G of binding of two protein 
inhibitors with similar structures). 

Examples on the size of T delta S are given in many publications discussing 
MM/PBSA and its variants - in the past we calculated absolute values that were 
in the same order of magnitude as delta G for a protein-peptide complex 
(http://dx.doi.org/10.1529/biophysj.106.085399).

I'm not familiar with Material Studio, but there are several methods to 
calculate entropy changes from MD simulations - quasi harmonic analysis is one 
that's implemented in Gromacs and Wordom. All have their limitations, but the 
same is true for experimental measurements of entropy changes upon binding.

Ran


Ran Friedman
Biträdande Lektor (Assistant Professor)

Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden

+46 480   44 6290 Telephone
+46   76 207 8763 Mobile
ran.fried...@lnu.se
http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Ehud Schreiber [schr...@compugen.co.il]
Sent: 21 October 2010 10:39
To: gmx-users@gromacs.org
Subject: [gmx-users] RE: Gibbs free energy of binding

Actually, I believe that using the energy difference, Delta E, as an
approximation to the free energy difference, Delta G, is a valid
approach (which I'm considering myself). The entropic contribution to
Delta G, namely -T Delta S, may be less prominent than Delta E.
In addition, Delta S can be approximated by various means - see e.g.
Doig & Sternberg 1995. I understand that such an approach is utilized in
the Accelrys Discovery Studio.
Obviously, this is an approximation that might be too crude for some
applications.

What do you think?


--

On Oct 21, 2010, at 09:25 , Sander Pronk wrote:

Hi Mohsen,

The mean energy difference is only one component of the free energy
difference.

Before you go any further I'd suggest reading a good book on molecular
simulations, like 'Understanding Molecular Simulations' by Frenkel and
Smit.

There's a good reason free energy calculations cover over half of that
book.

Sander


On Oct 21, 2010, at 09:18 , mohsen ramezanpour wrote:

> Dear Justin
>
> If I do  two  MD simulations for a short time in the same
conditions(of course separately for protein and drug)
>  and calculate total energy of each one and sum them with each other
as E1 as nonbonding free energy of system.
> then a MD simulation for Protein-drug system in the same condition and
calculate it's total energy too as E2 as bound system .
> what does (E1-E2)mean?
> I think it is binding free energy,Is not it?
> in the other hand when we are working on NPT ensamble it means Gibbs
free energy is the main energy and our total energy is equal to Gibbs
free energy.
> Then,what is the problem?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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[gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

[Carsten Kutzner]

Hi,

does anyone have experience with AMD's 12-core Magny-Cours
processors? With 48 cores on a node it is essential that the processes
are properly pinned to the cores for optimum performance.  Numactl
can do this, but at the moment I do not get good performance with
4.5.1 and threads, which still seem to be migrating around.

Carsten


--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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RE: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

[Berk Hess]

Hi,

We haven't observed any problems running with threads over 24 core AMD nodes 
(4x6 cores).

Berk

> From: ckut...@gwdg.de
> Date: Thu, 21 Oct 2010 12:03:00 +0200
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs
> 
> Hi,
> 
> does anyone have experience with AMD's 12-core Magny-Cours
> processors? With 48 cores on a node it is essential that the processes
> are properly pinned to the cores for optimum performance.  Numactl
> can do this, but at the moment I do not get good performance with
> 4.5.1 and threads, which still seem to be migrating around.
> 
> Carsten
> 
> 
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
> 
> 
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

[Sander Pronk]

Hi Carsten,

As Berk noted, we haven't had problems on 24-core machines, but quite frankly I 
haven't looked at thread migration. 

Currently, the wait states actively yield to the scheduler, which is an 
opportunity for the scheduler to re-assign threads to different cores. I could 
set harder thread affinity but that could compromise system responsiveness 
(when running mdrun on a desktop machine without active yielding, the system 
slows down noticeably). 

One thing you could try is to turn on the THREAD_MPI_WAIT_FOR_NO_ONE option in 
cmake. That turns off the yielding which might change the migration behavior.

BTW What do you mean with bad performance, and how do you notice thread 
migration issues?

Sander

On 21 Oct 2010, at 12:03 , Carsten Kutzner wrote:

> Hi,
> 
> does anyone have experience with AMD's 12-core Magny-Cours
> processors? With 48 cores on a node it is essential that the processes
> are properly pinned to the cores for optimum performance.  Numactl
> can do this, but at the moment I do not get good performance with
> 4.5.1 and threads, which still seem to be migrating around.
> 
> Carsten
> 
> 
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
> 
> 
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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[gmx-users] published paper related to protein simulation using gromacs

[ahmet yıldırım]

Dear Gromacs users,

I am new user Gromacs. I want to study on protein simulation using gromacs.
If possible, Can you send a few articles on the protein simulation using
Gromacs?For example, I downloaded from Protein Data Base the PDB extension
file of any protein. What is the purpose of protein simulation?What is
commonly the forcefied used for protein simulation? Which parameters are
calculated?... To answer these questions, I need the articles/papers written
in this area.
I will be happy if you help

Thanks in advance

-- 
Ahmet YILDIRIM
-- 
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Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

[Karel Berka]

>
>
> Karel Berka wrote:
> > Hi all,
> >
> > I have detected that preference in reading forcefield files in Gromacs
> > 4.5 has probably been changed from Gromacs 4.0.x and older.
> > In older gromacs, when there was forcefield with modification present in
> > my working directory, then it was read preferentially, but now it seems
> > that forcefield is primarily read from /share/top directory - Am I right?
> >
>
> The working directory is still searched first.
>

Unfortunately, it is not, otherwise ff in subdirectory of my working
directory would have been first one to use for grompp.
However, pdb2gmx was working fine for protein and ions around.

> In 4.5.2 I have tried to have modified gromos53a6.ff in my working
> > directory, but the modification was not used by gromacs.
> >
>
> What do you mean "not used"?  Was the wrong force field called when using
> pdb2gmx?


I did not used pdb2gmx since I am simulating membrane protein.
The only place when I needed to include forcefield itp was grompp program in
use on computer cluster , where I cannot reach /top directory


> Gromacs prints a list of force field subdirectories in the working
> directory, then in GMXLIB, and allows you to choose.  In the 4.5.x series,
> you
> need a full working subdirectory of the modified force field.
>
> FF.dat is not used anymore?

-Justin
>


-- 
Zdraví skoro zdravý
Karel "Krápník" Berka


RNDr. Karel Berka, Ph.D.
Palacký University in Olomouc
Faculty of Science
Department of Physical Chemistry
tř. 17. listopadu 1192/12
771 46 Olomouc
tel: +420-585634769
fax: +420-585634769
e-mail: karel.be...@upol.cz


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Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:

Hi justin

I found what went wrong and i corrected my mdp file.now the system 
equilibrated to the desired temperature 300 K (plus r minus 30 K) is 
this ok?


This is impossible to assess without seeing your .mdp settings.  A fluctuation 
of 10% is probably fine.


Apart from that i want to know how you plot the average running pressure 
and density in your tutorial for lyzosyme (redline). i just  want to do 
that for DCE. any help is highly appreciated.




Xmgrace.

-Justin


Regards
Vinoth

On Wed, Oct 20, 2010 at 5:33 PM, Justin A. Lemkul > wrote:




vinothkumar mohanakrishnan wrote:

Hi Justin

I corrected the mistake what you said and i am able to run
energy minimisation and equilibration. but when i view my em.gro
and equilibration.gro in VMD it seems to me that the bonds
between the atoms are broken in molecules.I used g_energy to
check weather the system has


VMD tries to guess where bonds should be, but does not always do a
good job. Your topology defines bonds.  These are the only bonds
that there will be.  None can be broken or formed in standard MD.


equilibrated to the required temperature (300K) i found that the
variation in the temperature was 100K (plus r minus) . i am not
able find out what went wrong. any help is highly appreciated.


Without seeing your .mdp file, there's no way to know.  The
fluctuation does seem too high, though, unless your system really is
just that unstable.  Are other properties converged - potential
energy, density, etc?  What type of ensemble are you using?

-Justin

Regards
Vinoth


On Mon, Oct 18, 2010 at 6:09 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   vinothkumar mohanakrishnan wrote:

   Dear Justin

   what corrections i should make to ffoplsaan.itp to make it
   correct. what i should give instead of CAB and CLAA?.


   You must use atom types, not names.  Unfortunately, you've
chosen to
   use atom names, which are also types, which makes all of this
quite
   confusing if you're not sure what you're doing.

   You defined two new atom types - opls_966 (CAB) and opls_967
(CLAA),
   which are the only indicators you are allowed to use if
introducing
   new types.  Thus, references to atom names (CAC, CLAD) will
generate
   fatal errors.


   i copied the .rtp .atp .itp files from
   usr/local/gromacs/share/gromacs/top to my working
directory and
   added these parameters to the corresponding files. what
you mean
   is should i need to add these parameters to the source
directory
   ( usr/local/gromacs/share/gromacs/top)?


   Your topology needs to be consistent with whatever files need
to be
   included. By default, Gromacs checks the working directory first,
   but if you've moved to a new (sub)directory to carry out further
   steps, the grompp will not find your modified files, but will
   instead locate only the default force field files in $GMXLIB.
Either keep all your work in one directory (which can get
messy),
   or make use of the "include" keyword in the .mdp file.  Any
   directory specified there will be searched after the working
   directory, but before $GMXLIB.

   -Justin

   Regards
   Vinoth


   On Mon, Oct 18, 2010 at 5:27 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

Re: [gmx-users] published paper related to protein simulation using gromacs

[Deniz KARASU]

Ahmet,

For starting you can read Leach's  book (Molecular modeling: principles and
applications). This book gives you theoretical background and opinion about
application areas of molecular dynamics (MD) simulation. Gromacs is only a
simulation tool to do MD simulation, after understanding MD you can use any
simulation tool (gromacs, namd, amber ..)  to do MD. Also you can look
some review papers on molecular dynamic simulation  like Lindahl's paper
(do:10.1007/978-1-59745-177-2_1),  Karplus's paper (doi:10.1038/nsb0902-646.) .
Lindahl's paper has a introduction format and prepared like tutorial for
gromacs. For more paper using gromacs you can search google scholor with
"gromacs" keyword.

deniz.

2010/10/21 ahmet yıldırım 

> Dear Gromacs users,
>
> I am new user Gromacs. I want to study on protein simulation using gromacs.
> If possible, Can you send a few articles on the protein simulation using
> Gromacs?For example, I downloaded from Protein Data Base the PDB extension
> file of any protein. What is the purpose of protein simulation?What is
> commonly the forcefied used for protein simulation? Which parameters are
> calculated?... To answer these questions, I need the articles/papers
> written in this area.
> I will be happy if you help
>
> Thanks in advance
>
> --
> Ahmet YILDIRIM
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

[Justin A. Lemkul]

Karel Berka wrote:


Karel Berka wrote:
 > Hi all,
 >
 > I have detected that preference in reading forcefield files in
Gromacs
 > 4.5 has probably been changed from Gromacs 4.0.x and older.
 > In older gromacs, when there was forcefield with modification
present in
 > my working directory, then it was read preferentially, but now it
seems
 > that forcefield is primarily read from /share/top directory - Am
I right?
 >

The working directory is still searched first. 

 
Unfortunately, it is not, otherwise ff in subdirectory of my working 
directory would have been first one to use for grompp. 
However, pdb2gmx was working fine for protein and ions around. 



My guess is that this is a matter of how the force field was #included in the 
.top file.  For instance:


#include "my.ff/forcefield.itp"

will match $GMXLIB first, but

#include "./my.ff/forcefield.itp"

will match the working directory first.  Is this perhaps the issue you're 
finding?  Other simple #include statements (like #include "ions.itp", etc) still 
use the old order of preference, but subdirectories make that a bit more difficult.



 > In 4.5.2 I have tried to have modified gromos53a6.ff in my working
 > directory, but the modification was not used by gromacs.
 >

What do you mean "not used"?  Was the wrong force field called when
using
pdb2gmx?  



I did not used pdb2gmx since I am simulating membrane protein. 
The only place when I needed to include forcefield itp was grompp 
program in use on computer cluster , where I cannot reach /top directory
 


Gromacs prints a list of force field subdirectories in the working
directory, then in GMXLIB, and allows you to choose.  In the 4.5.x
series, you
need a full working subdirectory of the modified force field.

FF.dat is not used anymore? 



No.  The list of force fields is populated from the *.ff entries in the working 
directory and $GMXLIB.


-Justin


-Justin



--
Zdraví skoro zdravý
Karel "Krápník" Berka


RNDr. Karel Berka, Ph.D.
Palacký University in Olomouc
Faculty of Science
Department of Physical Chemistry
tř. 17. listopadu 1192/12
771 46 Olomouc
tel: +420-585634769  
fax: +420-585634769

e-mail: karel.be...@upol.cz 





--


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


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[gmx-users] Re: published paper related to protein simulation, using gromacs

[Thomas Schlesier]

Hi,
use ISI Web of Knowledge or scholar.google, search for 'protein + 
gromacs' and you should get tons of results.

Greetings
Thomas



Date: Thu, 21 Oct 2010 13:29:11 +0300
From: ahmet y?ld?r?m
Subject: [gmx-users] published paper related to protein simulation
using   gromacs
To: Discussion list for GROMACS users
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Dear Gromacs users,

I am new user Gromacs. I want to study on protein simulation using gromacs.
If possible, Can you send a few articles on the protein simulation using
Gromacs?For example, I downloaded from Protein Data Base the PDB extension
file of any protein. What is the purpose of protein simulation?What is
commonly the forcefied used for protein simulation? Which parameters are
calculated?... To answer these questions, I need the articles/papers written
in this area.
I will be happy if you help

Thanks in advance

   


--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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RE: [gmx-users] Re: published paper related to protein simulation, using gromacs

[#ZHAO LINA#]

Hi,

I think, started from some gromacs tutorial is a nice ideas and then during 
those process you certainly will meet some paper. 

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Thomas Schlesier [schl...@uni-mainz.de]
Sent: Thursday, October 21, 2010 7:45 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: published paper related to protein simulation, using 
gromacs

Hi,
use ISI Web of Knowledge or scholar.google, search for 'protein +
gromacs' and you should get tons of results.
Greetings
Thomas


> Date: Thu, 21 Oct 2010 13:29:11 +0300
> From: ahmet y?ld?r?m
> Subject: [gmx-users] published paper related to protein simulation
>   using   gromacs
> To: Discussion list for GROMACS users
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Gromacs users,
>
> I am new user Gromacs. I want to study on protein simulation using gromacs.
> If possible, Can you send a few articles on the protein simulation using
> Gromacs?For example, I downloaded from Protein Data Base the PDB extension
> file of any protein. What is the purpose of protein simulation?What is
> commonly the forcefied used for protein simulation? Which parameters are
> calculated?... To answer these questions, I need the articles/papers written
> in this area.
> I will be happy if you help
>
> Thanks in advance
>
>

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Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

[vinothkumar mohanakrishnan]

Hi Justin

Below is my nvt.mdp (nvt equilibration) file.i think probably you can have
look at it and its not such big.

define  = -DFLEXIBLE
integrator =  md
nsteps =  5
dt=  0.002
nstxout=  100
nstvout=  100
nstenergy=  100
nstlog =  100
constraint_algorithm = shake
constraints=none
unconstrained_start=yes
shake_tol=  0.0001
morse=   no
ns_type=grid
nstlist=   5
rlist=  1.0
coulombtype=PME
rcoulomb=  1.0
vdwtype=   Cut-off
rvdw=1.0
pme_order=4
fourierspacing=  0.16
pbc= xyz
tcoupl= V-rescale
tc-grps=system
tau_t=   0.1
ref_t=   300
DispCorr= Ener
gen_vel=  yes
gen_temp=   300
gen_seed=   173529

regarding the plot i too know that one should use Xmgrace to plot. In the
pressure Vs time(lysozyme tutorial) you have got two graphs. i to got the
pressure Vs time (black line graph) my question is how to get the running
average ( red line) and plot?. does i need any command to get the running
average?. any help is highly appreciated.

Regards
Vinoth

On Thu, Oct 21, 2010 at 4:56 PM, Justin A. Lemkul  wrote:

>
>
> vinothkumar mohanakrishnan wrote:
>
>> Hi justin
>>
>> I found what went wrong and i corrected my mdp file.now the system
>> equilibrated to the desired temperature 300 K (plus r minus 30 K) is this
>> ok?
>>
>
> This is impossible to assess without seeing your .mdp settings.  A
> fluctuation of 10% is probably fine.
>
>
>  Apart from that i want to know how you plot the average running pressure
>> and density in your tutorial for lyzosyme (redline). i just  want to do that
>> for DCE. any help is highly appreciated.
>>
>>
> Xmgrace.
>
> -Justin
>
>  Regards
>> Vinoth
>>
>>
>> On Wed, Oct 20, 2010 at 5:33 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>vinothkumar mohanakrishnan wrote:
>>
>>Hi Justin
>>
>>I corrected the mistake what you said and i am able to run
>>energy minimisation and equilibration. but when i view my em.gro
>>and equilibration.gro in VMD it seems to me that the bonds
>>between the atoms are broken in molecules.I used g_energy to
>>check weather the system has
>>
>>
>>VMD tries to guess where bonds should be, but does not always do a
>>good job. Your topology defines bonds.  These are the only bonds
>>that there will be.  None can be broken or formed in standard MD.
>>
>>
>>equilibrated to the required temperature (300K) i found that the
>>variation in the temperature was 100K (plus r minus) . i am not
>>able find out what went wrong. any help is highly appreciated.
>>
>>
>>Without seeing your .mdp file, there's no way to know.  The
>>fluctuation does seem too high, though, unless your system really is
>>just that unstable.  Are other properties converged - potential
>>energy, density, etc?  What type of ensemble are you using?
>>
>>-Justin
>>
>>Regards
>>Vinoth
>>
>>
>>On Mon, Oct 18, 2010 at 6:09 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   vinothkumar mohanakrishnan wrote:
>>
>>   Dear Justin
>>
>>   what corrections i should make to ffoplsaan.itp to make it
>>   correct. what i should give instead of CAB and CLAA?.
>>
>>
>>   You must use atom types, not names.  Unfortunately, you've
>>chosen to
>>   use atom names, which are also types, which makes all of this
>>quite
>>   confusing if you're not sure what you're doing.
>>
>>   You defined two new atom types - opls_966 (CAB) and opls_967
>>(CLAA),
>>   which are the only indicators you are allowed to use if
>>introducing
>>   new types.  Thus, references to atom names (CAC, CLAD) will
>>generate
>>   fatal errors.
>>
>>
>>   i copied the .rtp .atp .itp files from
>>   usr/local/gromacs/share/gromacs/top to my working
>>directory and
>>   added these parameters to the corresponding files. what
>>you mean
>>   is should i need to add these parameters to the source
>>directory
>>   ( usr/local/gromacs/share/gromacs/top)?
>>
>>
>>   Your topology needs to be consistent with whatever files need
>>to be
>>   inc

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:

Hi Justin

Below is my nvt.mdp (nvt equilibration) file.i think probably you can 
have look at it and its not such big.


define  = -DFLEXIBLE 


You should never run MD with flexible water.  All the water models included in 
Gromacs are meant to be rigid.  -DFLEXIBLE should only be used during EM.


integrator =  md   
nsteps =  5  
dt=  0.002 
nstxout=  100  
nstvout=  100  
nstenergy=  100  
nstlog =  100   
constraint_algorithm = shake   
constraints=none   


If you're not using constraints, then a 2-fs timestep might be too large.  If 
you encounter any later instability, this is likely the cause.


unconstrained_start=yes  
shake_tol=  0.0001
morse=   no
ns_type=grid   
nstlist=   5   
rlist=  1.0  
coulombtype=PME   
rcoulomb=  1.0   
vdwtype=   Cut-off  
rvdw=1.0   
pme_order=4  
fourierspacing=  0.16   
pbc= xyz   
tcoupl= V-rescale   
tc-grps=system   
tau_t=   0.1   
ref_t=   300   
DispCorr= Ener  
gen_vel=  yes   
gen_temp=   300  
gen_seed=   173529   

regarding the plot i too know that one should use Xmgrace to plot. In 
the pressure Vs time(lysozyme tutorial) you have got two graphs. i to 
got the pressure Vs time (black line graph) my question is how to get 
the running average ( red line) and plot?. does i need any command to 
get the running average?. any help is highly appreciated.




Data -> Transformations -> Running averages

-Justin


Regards
Vinoth

On Thu, Oct 21, 2010 at 4:56 PM, Justin A. Lemkul > wrote:




vinothkumar mohanakrishnan wrote:

Hi justin

I found what went wrong and i corrected my mdp file.now the
system equilibrated to the desired temperature 300 K (plus r
minus 30 K) is this ok?


This is impossible to assess without seeing your .mdp settings.  A
fluctuation of 10% is probably fine.


Apart from that i want to know how you plot the average running
pressure and density in your tutorial for lyzosyme (redline). i
just  want to do that for DCE. any help is highly appreciated.


Xmgrace.

-Justin

Regards
Vinoth


On Wed, Oct 20, 2010 at 5:33 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   vinothkumar mohanakrishnan wrote:

   Hi Justin

   I corrected the mistake what you said and i am able to run
   energy minimisation and equilibration. but when i view my
em.gro
   and equilibration.gro in VMD it seems to me that the bonds
   between the atoms are broken in molecules.I used g_energy to
   check weather the system has


   VMD tries to guess where bonds should be, but does not always
do a
   good job. Your topology defines bonds.  These are the only bonds
   that there will be.  None can be broken or formed in standard MD.


   equilibrated to the required temperature (300K) i found
that the
   variation in the temperature was 100K (plus r minus) . i
am not
   able find out what went wrong. any help is highly
appreciated.


   Without seeing your .mdp file, there's no way to know.  The
   fluctuation does seem too high, though, unless your system
really is
   just that unstable.  Are other properties converged - potential
   energy, density, etc?  What type of ensemble are you using?

   -Justin

   Regards
   Vinoth


   On Mon, Oct 18, 2010 at 6:09 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

[Carsten Kutzner]

Hi Sander,

On Oct 21, 2010, at 12:27 PM, Sander Pronk wrote:

> Hi Carsten,
> 
> As Berk noted, we haven't had problems on 24-core machines, but quite frankly 
> I haven't looked at thread migration. 
I did not have any problems on 32-core machines as well, only on 48-core ones.
> 
> Currently, the wait states actively yield to the scheduler, which is an 
> opportunity for the scheduler to re-assign threads to different cores. I 
> could set harder thread affinity but that could compromise system 
> responsiveness (when running mdrun on a desktop machine without active 
> yielding, the system slows down noticeably). 
> 
> One thing you could try is to turn on the THREAD_MPI_WAIT_FOR_NO_ONE option 
> in cmake. That turns off the yielding which might change the migration 
> behavior.
I will try that, thanks!
> 
> BTW What do you mean with bad performance, and how do you notice thread 
> migration issues?
A while ago I benchmarked a ~80,000 atom test system (membrane+channel+water, 2 
fs time 
step, cutoffs @ 1 nm) on a 48-core 1.9 GHz AMD node. My first try gave a lousy 
7.5 ns/day 
using Gromacs 4.0.7 and IntelMPI. According to AMD, parallel applications 
should be
run under control of numactl to be compliant to the new memory hierarchy. Also, 
they
suggest using OpenMPI rather than other MPI libs. With OpenMPI and numactl - 
which pins
the processes to the cores - the performance was nearly doubled to 14.3 ns/day. 
Using 
Gromacs 4.5 I got 14.0 ns/day with OpenMPI+numactl and 15.2 ns/day with threads 
(here no 
pinning was necessary for the threaded version!)

Now on another machine with identical hardware (but another Linux) I get 4.5.1 
timings that 
vary a lot (see g_tune_pme snippet below) even between identical runs. One run 
actually approaches 
the expected 15 ns/day, while the others with also 20 PME-only nodes) do not. I 
cannot be shure
that thread migration is the problem here, but correct pinning might be 
necessary here. 

Carsten
 


g_tune_pme output snippet for mdrun with threads:
-
Benchmark steps : 1000
dlb equilibration steps : 100
Repeats for each test   : 4

 No.   scaling  rcoulomb  nkx  nky  nkz   spacing  rvdw  tpr file
   0   -input-  1.00   90   88   80  0.119865   1.00  
./Aquaporin_gmx4_bench00.tpr

Individual timings for input file 0 (./Aquaporin_gmx4_bench00.tpr):
PME nodes  Gcycles   ns/dayPME/fRemark
  24  1804.4428.7361.703OK.
  24  1805.6558.7301.689OK.
  24  1260.351   12.5050.647OK.
  24  1954.3148.0641.488OK.
  20  1753.3868.9921.960OK.
  20  1981.0327.9582.190OK.
  20  1344.375   11.7211.180OK.
  20  1103.340   14.2870.896OK.
  16  1876.1348.4041.713OK.
  16  1844.1118.5511.525OK.
  16  1757.4148.9721.845OK.
  16  1785.0508.8331.208OK.
   0  1851.6458.520  -  OK.
   0  1871.9558.427  -  OK.
   0  1978.3577.974  -  OK.
   0  1848.5158.534  -  OK.
  -1( 18) 1926.2028.1821.453OK.
  -1( 18) 1195.456   13.1840.826OK.
  -1( 18) 1816.7658.6771.853OK.
  -1( 18) 1218.834   12.9310.884OK.



> Sander
> 
> On 21 Oct 2010, at 12:03 , Carsten Kutzner wrote:
> 
>> Hi,
>> 
>> does anyone have experience with AMD's 12-core Magny-Cours
>> processors? With 48 cores on a node it is essential that the processes
>> are properly pinned to the cores for optimum performance.  Numactl
>> can do this, but at the moment I do not get good performance with
>> 4.5.1 and threads, which still seem to be migrating around.
>> 
>> Carsten
>> 
>> 

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Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:

Hi Justin

Thank you for your suggestion. I am doing equilibration of DCE (108 
molecules) alone in a box and there is no water molecule inside the box. 
cant i use -DFLEXIBLE for DCE?. by the way i will try your suggestion 
about xmgrace.




In that case, -DFLEXBILE will have no effect.  The bigger concern then is the 
potential stability issues of not using constraints and using a 2-fs timestep. 
It might be fine, but keep it in mind if you run into problems.


-Justin


Regards
Vinoth

On Thu, Oct 21, 2010 at 5:25 PM, Justin A. Lemkul > wrote:




vinothkumar mohanakrishnan wrote:

Hi Justin

Below is my nvt.mdp (nvt equilibration) file.i think probably
you can have look at it and its not such big.

define  = -DFLEXIBLE


You should never run MD with flexible water.  All the water models
included in Gromacs are meant to be rigid.  -DFLEXIBLE should only
be used during EM.


integrator =  md   nsteps =
 5  dt=
 0.002 nstxout=  100  nstvout  
 =  100  nstenergy=
 100  nstlog =  100  
constraint_algorithm = shake   constraints=
   none  



If you're not using constraints, then a 2-fs timestep might be too
large.  If you encounter any later instability, this is likely the
cause.


unconstrained_start=yes  shake_tol=
 0.0001
morse=   nons_type=
   grid   nstlist=   5  
rlist=  1.0  coulombtype=  
 PME   rcoulomb=  1.0  
vdwtype=   Cut-off  rvdw=  
 1.0   pme_order=4
 fourierspacing=  0.16   pbc=  
  xyz   tcoupl= V-rescale  
tc-grps=system   tau_t=
  0.1   ref_t=   300  
DispCorr= Ener  gen_vel=
 yes   gen_temp=   300  gen_seed=  
173529  
regarding the plot i too know that one should use Xmgrace to

plot. In the pressure Vs time(lysozyme tutorial) you have got
two graphs. i to got the pressure Vs time (black line graph) my
question is how to get the running average ( red line) and
plot?. does i need any command to get the running average?. any
help is highly appreciated.


Data -> Transformations -> Running averages

-Justin

Regards
Vinoth


On Thu, Oct 21, 2010 at 4:56 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   vinothkumar mohanakrishnan wrote:

   Hi justin

   I found what went wrong and i corrected my mdp file.now the
   system equilibrated to the desired temperature 300 K (plus r
   minus 30 K) is this ok?


   This is impossible to assess without seeing your .mdp
settings.  A
   fluctuation of 10% is probably fine.


   Apart from that i want to know how you plot the average
running
   pressure and density in your tutorial for lyzosyme
(redline). i
   just  want to do that for DCE. any help is highly
appreciated.


   Xmgrace.

   -Justin

   Regards
   Vinoth


   On Wed, Oct 20, 2010 at 5:33 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

[gmx-users] CHARMM36 lipid bilayers

[Sven Jakobtorweihen]

Dear gmx-users,

recently Pär Bjelkmar and Thomas Piggot have generated force field files
for Charmm36 lipids. I run some simulations to find the best run
parameters and to check if the results of the original Charmm36 lipid
article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be
reproduced with gromacs.

I run 40 ns NPT simulations with semiisotropic pressure coupling
(Parrinello-Rahman, tau_p=5),  the first 10 ns are equilibration and
averages were calculated for the last 30 ns. DMPC and POPC at 303 K and
DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with
pdb2gmx -nochargegrp. All simulations contained 128 lipids and
approximately the same water/lipid ratio (water is TIP3P) as Klauda et
al. I started from charmm27 bilayers provided at the Chramm Gui website.
I used the following parameters:

 rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME;
rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00;
nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002

These simulations result in the following area per lipid [A^2/lipid]:
DMPC=56.6 +/- 0.4  ; POPC =61.8 +/- 0.4 ;  DPPC=55.0 +/- 0.7

Comparing to the results of Klauda et al (all simulation with the
charmm-package, except one):
DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1
+/- 0.4 (with NAMD)

It is obvious that my simulations with gromacs 4.5.1 give lower areas
per lipid for all cases. Considering the deviations observed by Klauda
et al. between Charmm and NAMD simulations ( rvdw_switch was only
changed slightly in NAMD) could lead to the conclusion that DMPC and
POPC are fine. But I am a bit worried about the DPPC result. Did anyone
have suggestions how to improve it? Are these differences expected when
comparing gromacs and charmm simulations? Did by any chance someone else
tested charmm36 bilayers in gromacs?

Thanks,
Sven
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[gmx-users] gromacs+MOPAC QMMM error

[Andrea Coletta]

I have compiled a mdrun version of gromacs 4.0.7 linked with the mopac7 
libraries, as described in the tutorial:


***
export CC=gcc
export CXX=g++
export F77=gfortran
export MPICC=/apps/openmpi/1.4.2/gcc/bin/mpicc
export CPPFLAGS="-DUSE_MOPAC -I/apps/fftw/3.2.2/gcc/include 
-I/apps/gsl/1.9/gcc/include "
export LDFLAGS="-L/apps/fftw/3.2.2/gcc/lib -L/apps/openmpi/1.4.2/gcc/lib 
-L/apps/gsl/1.9/gcc/lib -L/apps/mopac"

export LIBS="-lmopac -lf2c -lgfortran"
make clean
./configure --prefix=/apps/gromacs/4.0.7/gcc  --with-qmmm-mopac 
--program-suffix=_mopac --with-gsl

make mdrun
make install-mdrun
***

everything is gone fine, but when I tried to run my simulation AM1|PM3 
mdrun gave this error:


***
[...]
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 33
QMlevel: AM1/STO-3G

  RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 46
keywords are: PRECISE GEO-OK CHARGE=0 GRAD MMOK ANALYT AM1

starting mdrun 'DIM Multi-RESP in water'
100 steps,  0.0 ps.
nr mm atoms in gaussian.c = 1536
Calling '(null)/(null) < input.com > input.log'
sh: Syntax error: word unexpected

---
Program mdrun_mopac, VERSION 4.0.7
Source code file: qm_gaussian.c, line: 906

Fatal error:
Call to '(null)/(null) < input.com > input.log' failed

---
***

It seems like mdrun is requesting a gaussian QM calculation.

So i re-compiled mdrun with different configuration:
./configure --prefix=/apps/gromacs/4.0.7/gcc  --with-qmmm-mopac 
--without-qmmm-gaussian --program-suffix=_mopac --with-gsl


but now the error is:

***
---
Program mdrun_mopac, VERSION 4.0.7
Source code file: qmmm.c, line: 191

Fatal error:
Ab-initio calculation only supported with Gamess or Gaussian.
---
***

What can be the solution?!

Thank you

Andrea Coletta
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[gmx-users] (no subject)

[Nilesh Dhumal]

Hello,
I am working on a system which has a diatomic solute surrounded by water
molecules.
I want to calculate the energy for each step with and with out charge on
solute simultaneously.
Pl. help me solve this problem.

Nilesh



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RE: [gmx-users] CHARMM36 lipid bilayers

[Berk Hess]

Hi,

You have very strange and complex cut-off settings in Gromacs.
What Charmm settings are you trying to mimic?

Berk

> Date: Thu, 21 Oct 2010 15:03:51 +0200
> From: jakobtorwei...@tuhh.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] CHARMM36 lipid bilayers
> 
> Dear gmx-users,
> 
> recently Pär Bjelkmar and Thomas Piggot have generated force field files
> for Charmm36 lipids. I run some simulations to find the best run
> parameters and to check if the results of the original Charmm36 lipid
> article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be
> reproduced with gromacs.
> 
> I run 40 ns NPT simulations with semiisotropic pressure coupling
> (Parrinello-Rahman, tau_p=5),  the first 10 ns are equilibration and
> averages were calculated for the last 30 ns. DMPC and POPC at 303 K and
> DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with
> pdb2gmx -nochargegrp. All simulations contained 128 lipids and
> approximately the same water/lipid ratio (water is TIP3P) as Klauda et
> al. I started from charmm27 bilayers provided at the Chramm Gui website.
> I used the following parameters:
> 
>  rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME;
> rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00;
> nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002
> 
> These simulations result in the following area per lipid [A^2/lipid]:
> DMPC=56.6 +/- 0.4  ; POPC =61.8 +/- 0.4 ;  DPPC=55.0 +/- 0.7
> 
> Comparing to the results of Klauda et al (all simulation with the
> charmm-package, except one):
> DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1
> +/- 0.4 (with NAMD)
> 
> It is obvious that my simulations with gromacs 4.5.1 give lower areas
> per lipid for all cases. Considering the deviations observed by Klauda
> et al. between Charmm and NAMD simulations ( rvdw_switch was only
> changed slightly in NAMD) could lead to the conclusion that DMPC and
> POPC are fine. But I am a bit worried about the DPPC result. Did anyone
> have suggestions how to improve it? Are these differences expected when
> comparing gromacs and charmm simulations? Did by any chance someone else
> tested charmm36 bilayers in gromacs?
> 
> Thanks,
> Sven
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
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[gmx-users] (no subject)

[Nilesh Dhumal]

Hello,
I am working on a system which has a diatomic solute surrounded by water
molecules.
I want to calculate the energy for each step with and with out charge on
solute simultaneously.
Pl. help me solve this problem.

Nilesh


-- 
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Re: [gmx-users] CHARMM36 lipid bilayers

[Sven Jakobtorweihen]

Hi Berk,

the original charmm article used
rvdw=1.2
rvdw_switch=0.8
coulombtype= PME
Unfortunately, they did not specify rcoulomb explicitly. In  the
discussions they  wrote ".. simulations of bilayers with C36 should be
carried out with PME  with rc=10 or 12 A and no long-range corrections
for the LJ term." I tested also  with rcoulomb=1.2, but the results were
closer to Klauda with rcoulomb=1.0. However, I think by adjusting
fourierspacing and pme_order I probably could get the same results with
rcoulomb=1.2 as with rcoulomb=1.0.

rlistlong=1.4 I set to avoid the note that it should be 0.1 to 0.3 nm
larger than rvdw. I realized that g_tune always sets rlistlong to the
largest cutoff and, hence, ignores the note. Considering efficiency I
would from now on use rlistlong=1.3 and if someone could convience me to
ignore the note I would go with 1.2. By the way, when g_tune changes
rlistlong in the tpr files where the load is shifted from the reciprocal
to the real space part the most (if not all) performance gain compared
to the original tpr comes from the rlistlong change.

See you,
Sven


Berk Hess schrieb:
> Hi,
>
> You have very strange and complex cut-off settings in Gromacs.
> What Charmm settings are you trying to mimic?
>
> Berk
>
> > Date: Thu, 21 Oct 2010 15:03:51 +0200
> > From: jakobtorwei...@tuhh.de
> > To: gmx-users@gromacs.org
> > Subject: [gmx-users] CHARMM36 lipid bilayers
> >
> > Dear gmx-users,
> >
> > recently Pär Bjelkmar and Thomas Piggot have generated force field files
> > for Charmm36 lipids. I run some simulations to find the best run
> > parameters and to check if the results of the original Charmm36 lipid
> > article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be
> > reproduced with gromacs.
> >
> > I run 40 ns NPT simulations with semiisotropic pressure coupling
> > (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and
> > averages were calculated for the last 30 ns. DMPC and POPC at 303 K and
> > DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with
> > pdb2gmx -nochargegrp. All simulations contained 128 lipids and
> > approximately the same water/lipid ratio (water is TIP3P) as Klauda et
> > al. I started from charmm27 bilayers provided at the Chramm Gui website.
> > I used the following parameters:
> >
> > rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME;
> > rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00;
> > nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002
> >
> > These simulations result in the following area per lipid [A^2/lipid]:
> > DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7
> >
> > Comparing to the results of Klauda et al (all simulation with the
> > charmm-package, except one):
> > DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1
> > +/- 0.4 (with NAMD)
> >
> > It is obvious that my simulations with gromacs 4.5.1 give lower areas
> > per lipid for all cases. Considering the deviations observed by Klauda
> > et al. between Charmm and NAMD simulations ( rvdw_switch was only
> > changed slightly in NAMD) could lead to the conclusion that DMPC and
> > POPC are fine. But I am a bit worried about the DPPC result. Did anyone
> > have suggestions how to improve it? Are these differences expected when
> > comparing gromacs and charmm simulations? Did by any chance someone else
> > tested charmm36 bilayers in gromacs?
> >
> > Thanks,
> > Sven
> > --
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Re: [gmx-users] (no subject)

[Mark Abraham]

On 21/10/2010 11:55 PM, Nilesh Dhumal wrote:

Hello,
I am working on a system which has a diatomic solute surrounded by water
molecules.
I want to calculate the energy for each step with and with out charge on
solute simultaneously.
Pl. help me solve this problem.


I don't understand what you want to do.

Mark
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Re: [gmx-users] (no subject)

[Nilesh Dhumal]

I am doing solvation dynamics for my system.
I have system with diatomic (PA---NE)solute surrounded by water molecules.

I want to run simulation with two differcent cases.
1. PA charge=0 and NE charge=0 : No charge on solute
2. PA charge=+1 and NE charge=-1 : Charge on solute

I want to calculate the energy at each step keeping the solvent
configration same.

IF I start a simulation with no charge on solute (case1), I have the
energy for 1 step. I want to calculate the energy with charge on solute
(case 2) with same configration water molecules.
Each step  I want to calculate the energy with and without charge on
solute since the configration of solvent will be same for that step.

I was thinking two make two topologies file with charge and with out
charge on solute. I don't know how to use them simultaneously during the
simulation.

NIlesh

On Thu, October 21, 2010 10:03 am, Mark Abraham wrote:
> On 21/10/2010 11:55 PM, Nilesh Dhumal wrote:
>
>> Hello,
>> I am working on a system which has a diatomic solute surrounded by water
>>  molecules. I want to calculate the energy for each step with and with
>> out charge on solute simultaneously. Pl. help me solve this problem.
>>
>
> I don't understand what you want to do.
>
>
> Mark
> --
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>
>


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Re: [gmx-users] (no subject)

[Justin A. Lemkul]

Nilesh Dhumal wrote:

I am doing solvation dynamics for my system.
I have system with diatomic (PA---NE)solute surrounded by water molecules.

I want to run simulation with two differcent cases.
1. PA charge=0 and NE charge=0 : No charge on solute
2. PA charge=+1 and NE charge=-1 : Charge on solute

I want to calculate the energy at each step keeping the solvent
configration same.

IF I start a simulation with no charge on solute (case1), I have the
energy for 1 step. I want to calculate the energy with charge on solute
(case 2) with same configration water molecules.
Each step  I want to calculate the energy with and without charge on
solute since the configration of solvent will be same for that step.

I was thinking two make two topologies file with charge and with out
charge on solute. I don't know how to use them simultaneously during the
simulation.



You can't.  Probably the best option is to do an mdrun -rerun using the second 
topology.


-Justin


NIlesh

On Thu, October 21, 2010 10:03 am, Mark Abraham wrote:

On 21/10/2010 11:55 PM, Nilesh Dhumal wrote:


Hello,
I am working on a system which has a diatomic solute surrounded by water
 molecules. I want to calculate the energy for each step with and with
out charge on solute simultaneously. Pl. help me solve this problem.


I don't understand what you want to do.


Mark
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] (no subject)

[Mark Abraham]

On 22/10/2010 1:17 AM, Nilesh Dhumal wrote:

I am doing solvation dynamics for my system.
I have system with diatomic (PA---NE)solute surrounded by water molecules.

I want to run simulation with two differcent cases.
1. PA charge=0 and NE charge=0 : No charge on solute
2. PA charge=+1 and NE charge=-1 : Charge on solute

I want to calculate the energy at each step keeping the solvent
configration same.

IF I start a simulation with no charge on solute (case1), I have the
energy for 1 step. I want to calculate the energy with charge on solute
(case 2) with same configration water molecules.
Each step  I want to calculate the energy with and without charge on
solute since the configration of solvent will be same for that step.

I was thinking two make two topologies file with charge and with out
charge on solute. I don't know how to use them simultaneously during the
simulation.


Well, you don't use them simultaneously. You run a simulation on 
whatever you think will generate a relevant conformational ensemble. 
Then you want to use mdrun -rerun twice on the resulting trajectory, 
using .tpr files based on .top files corresponding to the two cases in 
order to create your comparison.


Mark
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Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

[Sander Pronk]

Thanks for the information; the OpenMPI recommendation is probably because 
OpenMPI goes to great lengths trying to avoid process migration. The numactl 
doesn't prevent migration as far as I can tell: it controls where memory gets 
allocated if it's NUMA. 

For gromacs the setting should of course always be
numactl --localalloc

As far as thread migration goes: that might also be a kernel issue. If I 
remember correctly, this issue has only recently been addressed in the Linux 
kernel. I'll check whether there's anything we can do specifically for Gromacs.

Sander


On 21 Oct 2010, at 14:04 , Carsten Kutzner wrote:

> Hi Sander,
> 
> On Oct 21, 2010, at 12:27 PM, Sander Pronk wrote:
> 
>> Hi Carsten,
>> 
>> As Berk noted, we haven't had problems on 24-core machines, but quite 
>> frankly I haven't looked at thread migration. 
> I did not have any problems on 32-core machines as well, only on 48-core ones.
>> 
>> Currently, the wait states actively yield to the scheduler, which is an 
>> opportunity for the scheduler to re-assign threads to different cores. I 
>> could set harder thread affinity but that could compromise system 
>> responsiveness (when running mdrun on a desktop machine without active 
>> yielding, the system slows down noticeably). 
>> 
>> One thing you could try is to turn on the THREAD_MPI_WAIT_FOR_NO_ONE option 
>> in cmake. That turns off the yielding which might change the migration 
>> behavior.
> I will try that, thanks!
>> 
>> BTW What do you mean with bad performance, and how do you notice thread 
>> migration issues?
> A while ago I benchmarked a ~80,000 atom test system (membrane+channel+water, 
> 2 fs time 
> step, cutoffs @ 1 nm) on a 48-core 1.9 GHz AMD node. My first try gave a 
> lousy 7.5 ns/day 
> using Gromacs 4.0.7 and IntelMPI. According to AMD, parallel applications 
> should be
> run under control of numactl to be compliant to the new memory hierarchy. 
> Also, they
> suggest using OpenMPI rather than other MPI libs. With OpenMPI and numactl - 
> which pins
> the processes to the cores - the performance was nearly doubled to 14.3 
> ns/day. Using 
> Gromacs 4.5 I got 14.0 ns/day with OpenMPI+numactl and 15.2 ns/day with 
> threads (here no 
> pinning was necessary for the threaded version!)
> 
> Now on another machine with identical hardware (but another Linux) I get 
> 4.5.1 timings that 
> vary a lot (see g_tune_pme snippet below) even between identical runs. One 
> run actually approaches 
> the expected 15 ns/day, while the others with also 20 PME-only nodes) do not. 
> I cannot be shure
> that thread migration is the problem here, but correct pinning might be 
> necessary here. 
> 
> Carsten
> 
> 
> 
> g_tune_pme output snippet for mdrun with threads:
> -
> Benchmark steps : 1000
> dlb equilibration steps : 100
> Repeats for each test   : 4
> 
> No.   scaling  rcoulomb  nkx  nky  nkz   spacing  rvdw  tpr file
>   0   -input-  1.00   90   88   80  0.119865   1.00  
> ./Aquaporin_gmx4_bench00.tpr
> 
> Individual timings for input file 0 (./Aquaporin_gmx4_bench00.tpr):
> PME nodes  Gcycles   ns/dayPME/fRemark
>  24  1804.4428.7361.703OK.
>  24  1805.6558.7301.689OK.
>  24  1260.351   12.5050.647OK.
>  24  1954.3148.0641.488OK.
>  20  1753.3868.9921.960OK.
>  20  1981.0327.9582.190OK.
>  20  1344.375   11.7211.180OK.
>  20  1103.340   14.2870.896OK.
>  16  1876.1348.4041.713OK.
>  16  1844.1118.5511.525OK.
>  16  1757.4148.9721.845OK.
>  16  1785.0508.8331.208OK.
>   0  1851.6458.520  -  OK.
>   0  1871.9558.427  -  OK.
>   0  1978.3577.974  -  OK.
>   0  1848.5158.534  -  OK.
>  -1( 18) 1926.2028.1821.453OK.
>  -1( 18) 1195.456   13.1840.826OK.
>  -1( 18) 1816.7658.6771.853OK.
>  -1( 18) 1218.834   12.9310.884OK.
> 
> 
> 
>> Sander
>> 
>> On 21 Oct 2010, at 12:03 , Carsten Kutzner wrote:
>> 
>>> Hi,
>>> 
>>> does anyone have experience with AMD's 12-core Magny-Cours
>>> processors? With 48 cores on a node it is essential that the processes
>>> are properly pinned to the cores for optimum performance.  Numactl
>>> can do this, but at the moment I do not get good performance with
>>> 4.5.1 and threads, which still seem to be migrating around.
>>> 
>>> Carsten
>>> 
>>> 
> 
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Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

[Carsten Kutzner]

On Oct 21, 2010, at 4:44 PM, Sander Pronk wrote:

> 
> Thanks for the information; the OpenMPI recommendation is probably because 
> OpenMPI goes to great lengths trying to avoid process migration. The numactl 
> doesn't prevent migration as far as I can tell: it controls where memory gets 
> allocated if it's NUMA. 
My understanding is that processes get pinned to cores with the help of 
the --physcpubind switch to numactl, but please correct me if I am wrong.
 
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Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

[Sander Pronk]

On 21 Oct 2010, at 16:50 , Carsten Kutzner wrote:

> On Oct 21, 2010, at 4:44 PM, Sander Pronk wrote:
> 
>> 
>> Thanks for the information; the OpenMPI recommendation is probably because 
>> OpenMPI goes to great lengths trying to avoid process migration. The numactl 
>> doesn't prevent migration as far as I can tell: it controls where memory 
>> gets allocated if it's NUMA. 
> My understanding is that processes get pinned to cores with the help of 
> the --physcpubind switch to numactl, but please correct me if I am wrong.
> 

The documentation isn't clear on that: you bind a process to a set of cores, 
but that wouldn't necessarily mean that threads that belong to that process are 
bound to a specific core. They might be allowed to migrate within the set that 
you give the process.


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Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

[Esztermann, Ansgar]

>>> Thanks for the information; the OpenMPI recommendation is probably because 
>>> OpenMPI goes to great lengths trying to avoid process migration. The 
>>> numactl doesn't prevent migration as far as I can tell: it controls where 
>>> memory gets allocated if it's NUMA. 
>> My understanding is that processes get pinned to cores with the help of 
>> the --physcpubind switch to numactl, but please correct me if I am wrong.
>> 
> 
> The documentation isn't clear on that: you bind a process to a set of cores, 
> but that wouldn't necessarily mean that threads that belong to that process 
> are bound to a specific core. They might be allowed to migrate within the set 
> that you give the process.

I've just checked a short (a few seconds) benchmark run -- I didn't observe any 
migrations with or without numactl.


A.

-- 
Ansgar Esztermann
DV-Systemadministration
Max-Planck-Institut für biophysikalische Chemie, Abteilung 105

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Re: [gmx-users] CHARMM36 lipid bilayers

[Thomas Piggot]

Hi Sven,

I have also seen similar things from the area per lipid of the bilayers
I have run (POPC and DPPC). I would suggest you try running with the
CHARMM TIP3P water (tips3p.itp) and see if you get values which are
closer to the ones published in the paper you mention. This will be
discussed in a paper which we hope to have published fairly soon.

Cheers

Tom

Sven Jakobtorweihen wrote:

Dear gmx-users,

recently Pär Bjelkmar and Thomas Piggot have generated force field files
for Charmm36 lipids. I run some simulations to find the best run
parameters and to check if the results of the original Charmm36 lipid
article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be
reproduced with gromacs.

I run 40 ns NPT simulations with semiisotropic pressure coupling
(Parrinello-Rahman, tau_p=5),  the first 10 ns are equilibration and
averages were calculated for the last 30 ns. DMPC and POPC at 303 K and
DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with
pdb2gmx -nochargegrp. All simulations contained 128 lipids and
approximately the same water/lipid ratio (water is TIP3P) as Klauda et
al. I started from charmm27 bilayers provided at the Chramm Gui website.
I used the following parameters:

 rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME;
rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00;
nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002

These simulations result in the following area per lipid [A^2/lipid]:
DMPC=56.6 +/- 0.4  ; POPC =61.8 +/- 0.4 ;  DPPC=55.0 +/- 0.7

Comparing to the results of Klauda et al (all simulation with the
charmm-package, except one):
DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1
+/- 0.4 (with NAMD)

It is obvious that my simulations with gromacs 4.5.1 give lower areas
per lipid for all cases. Considering the deviations observed by Klauda
et al. between Charmm and NAMD simulations ( rvdw_switch was only
changed slightly in NAMD) could lead to the conclusion that DMPC and
POPC are fine. But I am a bit worried about the DPPC result. Did anyone
have suggestions how to improve it? Are these differences expected when
comparing gromacs and charmm simulations? Did by any chance someone else
tested charmm36 bilayers in gromacs?

Thanks,
Sven


--
Dr Thomas Piggot
University of Southampton, UK.

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Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

[Ondrej Marsalek]

Hi,

FWIW, I have recently asked about this in the hwloc mailing list:

http://www.open-mpi.org/community/lists/hwloc-users/2010/10/0232.php

In general, hwloc is a useful tool for these things.

http://www.open-mpi.org/projects/hwloc/

Best,
Ondrej


On Thu, Oct 21, 2010 at 12:03, Carsten Kutzner  wrote:
> Hi,
>
> does anyone have experience with AMD's 12-core Magny-Cours
> processors? With 48 cores on a node it is essential that the processes
> are properly pinned to the cores for optimum performance.  Numactl
> can do this, but at the moment I do not get good performance with
> 4.5.1 and threads, which still seem to be migrating around.
>
> Carsten
>
>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
>
>
>
>
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[gmx-users] g_dipole ? => The salt molecule => The discrepancy of dipole moment between my calculation and GROMACS

[Chih-Ying Lin]

HI

dipole moment = 48.0 sum of q_i x_i
x_i is the atomic position.
The PBC is considered.


I did not include the counter ion of the salt molecule in my calculation.
The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans.
Here "A" are a string of atoms, most of them are carbons.



For the cis-structure
Dipole moment from GROMACS
Average = 33.0312
Std. Dev. = 3.5144
Error = 0.0236
Dipole moment from my calculation = 55.8675



For the trans-structure
Dipole moment from GROMACS
Average = 36.8470
Std. Dev. = 3.4917
Error = 0.0238
Dipole moment from my calculation = 77.2346



Questions:
1. There is a huge discrepancy between my calculation results and GROMACS.
Or, the two results are within acceptable discrepancy ???

2. In the beginning, I suppose that the trans-structure has smaller dipole
moment than cis-structure. However, it seems to be the opposite conclusion
based on both GROMACS and my calculation. Is there something possible wrong
???

3. I get the partial charges from the Journal papers and the partial charges
are derived for the similar molecules as mine. Is that wrong?




Thank you
Lin









Hey Lin,

Did you consider PBC?
Also, I wouldn't include the bromide if I were you, as it just adds noise,
because it can move around freely. You seem to be interested in the change
in dipole moment in the cation only, anyway.

Cheers,

Tsjerk

On Oct 21, 2010 7:02 AM, "Chih-Ying Lin"  wrote:



HI
dipole moment = 48.0 sum of q_i x_i
x_i is the atomic position.

I did not include the counter ion of the salt molecule in my calculation.
The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans.
Here "A" are a string of atoms, most of them are carbons.



For the cis-structure
Dipole moment from GROMACS
Average = 33.0312
Std. Dev. = 3.5144
Error = 0.0236
Dipole moment from my calculation = 55.8675



For the trans-structure
Dipole moment from GROMACS
Average = 36.8470
Std. Dev. = 3.4917
Error = 0.0238
Dipole moment from my calculation = 77.2346



Questions:
1. There is a huge discrepancy between my calculation results and GROMACS.
Or, the two results are within acceptable discrepancy ???

2. In the beginning, I suppose that the trans-structure has smaller dipole
moment than cis-structure. However, it seems to be the opposite conclusion
based on both GROMACS and my calculation. Is there something possible wrong
???

3. I get the partial charges from the Journal papers and the partial charges
are derived for the similar molecules as mine. Is that wrong?




Thank you
Lin
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[gmx-users] Problems with NVT simulation with CHARMM27

[sa]

Dear All,

I am trying to equilibrate in NVT ensemble of a peptide with glycolipid (GL)
molecules in a cubic box filled with TIP3P water (from Mackerell et al.).
The force field for GL were converted to GROMACS format from CHARMM27 force
field with additional parameters non present in the forcefield added in
lipids.rtp, ffbonded.itp and ffnonboded.itp files.

I use the git version of GMX4.5.1 downloaded yesterday.

I can minimize successfully the system with the following em.mdp before to
perform the nvt run

--- em.mdp

title= Glyco + peptide in water
; Preprocessor - specify a full path if necessary.
cpp  = cpp
include  = -I../top
define   = -DFLEXIBLE
integrator  = steep
;nstcgsteep  = 1
emstep  = 0.01
emtol   = 400.0
;dt = 0.002
pbc = xyz
nsteps  = 1
nstlist = 1
ns_type = grid
vdw-type= Cut-off  ; twin range cut-off’s with neighbor
list
rlistlong   = 1.0
coulombtype = PME
rcoulomb= 1.0
rvdw= 1.2
;fourierspacing = 0.12
;pme_order  = 4
;ewald_rtol = 1e-05
;optimize_fft   = yes


I obtained the final energies :

   Energies (kJ/mol)
   Bond  AngleU-BProper Dih.  Improper Dih.
3.65918e+041.86096e+046.02333e+033.68911e+048.61501e+00
  CMAP Dih.  LJ-14 Coulomb-14LJ (SR)LJ (LR)
   -1.31952e+021.17641e+041.76586e+051.84759e+05   -1.92541e+03
   Coulomb (SR)   Coul. recip.  Potential Pressure (bar)
   -1.26284e+06   -1.61597e+05   -9.55265e+050.0e+00


Steepest Descents converged to Fmax < 400 in 518 steps
Potential Energy  = -9.5526519e+05
Maximum force =  3.7991144e+02 on atom 313
Norm of force =  9.2632399e+00

When I try to do the NVT equilibration step at 300 K with the following
nvt.mdp, the simulation crashed quickly (app. after 20 ps of run) with
several LINCS warnings for TIP3 water atoms

--- nvt.mdp
title   = Glyco + peptide in water
define  = -DPOSRES  ; position restrain for the peptide
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 24000 ; 2 * 5 = 100 ps
; to test
dt  = 0.001 ; 2 fs
; Output control
nstxout = 1000  ; save coordinates every 0.2 ps
nstvout = 1 ; save velocities every 0.2 ps
nstenergy   = 1 ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
energygrps  = Protein Non-Protein
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
vdw-type= Cut-off   ; twin range cut-off’s with neighbor list
rlistlong   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.12  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; one coupling groups - more
accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one for each group,
in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

- Here the message obtained

step 1499: Water molecule starting at atom 47947 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

Step 1500:
The charge group starting at atom 36 moved than the distance allowed by the
domain decomposition (1.20) in direction Y
distance out of cell -14795603.00
Old coordinates:5.1595.1153.453
New coordinates: 8325234.000 -1

[gmx-users] g_dipole ? => dipole moment => trans-structure is more hydrophobic than the cis-structure ?

[Chih-Ying Lin]

Hi
In one paper, the salt-molecule has two structures, trans and cis.
The sentence in the paper is that trans-structure is more hydrophobic than
the cis-structure without providing the value of the dipole moment.



I wonder know if the value of dipole moment is the main indicator to decide
if trans-structure is more hydrophobic than the cis-structure.
Also, is it all true for salt-molecule that trans-structure is more
hydrophobic than the cis-structure ?




Thank you
Lin
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Re: [gmx-users] RE: Gibbs free energy of binding

[mohsen ramezanpour]

reading your idea:
it seems to me I can't ignore entropy contribution because  my simulation is
at room tempreture.
Really I couldn't understand what can I do!
I am working at room tempreture and I want to estimate binding free
energy(delta G),can I ignore entropy in this simulation and calculate
binding free energy by the method that I said in my last email?
what do you think?
thank in advance for  your guid


On Thu, Oct 21, 2010 at 12:15 PM, David van der Spoel
wrote:

> On 2010-10-21 10.39, Ehud Schreiber wrote:
>
>> Actually, I believe that using the energy difference, Delta E, as an
>> approximation to the free energy difference, Delta G, is a valid
>> approach (which I'm considering myself). The entropic contribution to
>> Delta G, namely -T Delta S, may be less prominent than Delta E.
>> In addition, Delta S can be approximated by various means - see e.g.
>> Doig&  Sternberg 1995. I understand that such an approach is utilized in
>> the Accelrys Discovery Studio.
>> Obviously, this is an approximation that might be too crude for some
>> applications.
>>
>
> As a simple example the hydrophobic effect at room temperature is largely
> due to the entropy of the water [ at high temp it is due to the enthalpy of
> the water ].
>
> Since the hydrophobic effect is involved in all ligand binding it seems
> quite hopeless to get any reliable numbers when neglecting entropy. No
> referee will buy that - I wouldn't.
>
>
>
>> What do you think?
>>
>> 
>> --
>>
>> On Oct 21, 2010, at 09:25 , Sander Pronk wrote:
>>
>> Hi Mohsen,
>>
>> The mean energy difference is only one component of the free energy
>> difference.
>>
>> Before you go any further I'd suggest reading a good book on molecular
>> simulations, like 'Understanding Molecular Simulations' by Frenkel and
>> Smit.
>>
>> There's a good reason free energy calculations cover over half of that
>> book.
>>
>> Sander
>>
>>
>> On Oct 21, 2010, at 09:18 , mohsen ramezanpour wrote:
>>
>>  Dear Justin
>>>
>>> If I do  two  MD simulations for a short time in the same
>>>
>> conditions(of course separately for protein and drug)
>>
>>>  and calculate total energy of each one and sum them with each other
>>>
>> as E1 as nonbonding free energy of system.
>>
>>> then a MD simulation for Protein-drug system in the same condition and
>>>
>> calculate it's total energy too as E2 as bound system .
>>
>>> what does (E1-E2)mean?
>>> I think it is binding free energy,Is not it?
>>> in the other hand when we are working on NPT ensamble it means Gibbs
>>>
>> free energy is the main energy and our total energy is equal to Gibbs
>> free energy.
>>
>>> Then,what is the problem?
>>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>
> --
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[gmx-users] GPU slower than I7

[Renato Freitas]

Hi gromacs users,

I have installed the lastest version of gromacs (4.5.1) in an i7 980X
(6 cores or 12 with HT on; 3.3 GHz) with 12GB of RAM and compiled its
mpi version. Also I compiled the GPU-accelerated
version of gromacs. Then I did a  2 ns simulation using a small system
(11042 atoms)  to compare the performance of mdrun-gpu vs mdrun_mpi.
The results that I got are bellow:


My *.mdp is:

constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  100  ; total 2000 ps.
nstlist             =  10
ns_type             =  grid
coulombtype    = PME
rvdw                = 0.9
rlist               = 0.9
rcoulomb            = 0.9
fourierspacing      = 0.10
pme_order           = 4
ewald_rtol          = 1e-5
vdwtype             =  cut-off
pbc                 =  xyz
epsilon_rf    =  0
comm_mode           =  linear
nstxout             =  1000
nstvout             =  0
nstfout             =  0
nstxtcout           =  1000
nstlog              =  1000
nstenergy           =  1000
; Berendsen temperature coupling is on in four groups
tcoupl              = berendsen
tc-grps             = system
tau-t               = 0.1
ref-t               = 298
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 298 K.
gen_vel = no


RUNNING GROMACS ON GPU

mdrun-gpu -s topol.tpr -v > & out &

Here is a part of the md.log:

Started mdrun on node 0 Wed Oct 20 09:52:09 2010
.
.
.
 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes   Number  G-CyclesSeconds %
--
 Write traj.1   1021106.075 31.7
0.2
 Rest   1   64125.577   19178.6 99.8
--
 Total  1   64231.652   19210.3 100.0
--

NODE (s)Real (s)(%)
   Time:6381.84019210.349   33.2
   1h46:21
(Mnbf/s)   (MFlops) (ns/day)(hour/ns)
Performance:0.000   0.001   27.077  0.886

Finished mdrun on node 0 Wed Oct 20 15:12:19 2010


RUNNING GROMACS ON MPI

mpirun -np 6 mdrun_mpi -s topol.tpr -npme 3 -v > & out &

Here is a part of the md.log:

Started mdrun on node 0 Wed Oct 20 18:30:52 2010

 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes   Number  G-CyclesSeconds %
--
 Domain decomp. 3  11 1452.166  434.7 0.6
 DD comm. load  3  100010.745  0.2
   0.0
 Send X to PME 3  101249.003   74.5
  0.1
 Comm. coord.   3  101   637.329190.8
  0.3
 Neighbor search3  11 8738.669  2616.0
 3.5
 Force   3  101   99210.202
29699.239.2
 Wait + Comm. F   3  101   3361.591   1006.3 1.3
 PME mesh   3  101   66189.554 19814.2
   26.2
 Wait + Comm. X/F3  60294.513 8049.5  23.8
 Wait + Recv. PME F 3  101801.897240.1   0.3
 Write traj. 3  1015 33.464
  10.0 0.0
 Update 3  1013295.820
986.6  1.3
 Constraints  3  101 6317.568
1891.2  2.5
 Comm. energies   3  12  70.784  21.2
   0.0
 Rest3  2314.844
693.0   0.9
--
 Total6  252968.14875727.5
 100.0
--
--
 PME redist. X/F3  2021945.551  582.4
  0.8
 PME spread/gather   3  20237219.60711141.914.7
 PME 3D-FFT3  20221453.362 6422.2
8.5
 PME solve   3   

[gmx-users] g_dipole ? =>salt-molecule => the relative position of counter ions to the rest of salt-molecule matters ???

[Chih-Ying Lin]

HI


As Timo M.D. Graen described
"As long as the system is neutral, the reference point will not affect the
calculation result of the dipole moment for the system."

On the other hand, I also play around the small salt-molecule as Timo M.D.
Graen suggested.
"take two ions for a start, Na+ and Cl-, place
them at NA(1,1,0) and CL(2,1,0). Now calculate the dipole moment for
this system using different points of reference, i.e. (0,0,0) and
(1,2,0) and (3,3,0). What do you observe? Next, add an additional NA+
ion to your system at NA(3,1,0) and repeat your calculation for the same
reference points. "



So, i include the counter ion in my dipole moment-calculation this time.
But, the dipole moment of the system depends on where the counter ions are
located.
For the cis-structure, the dipole moment is range from 45 to 75 as I
randomly set the position of the counter ions.
For the trans-structure, the dipole is range from 35 to 77 as I randomly set
the position of the counter ions.



I have used GROMACS to test the dipole moment of the similar systems where
GROMACS set the positions of the counter ions and the rest of molecules.
For the cis-structure, the dipole moment is around 33.  The standard
deviation ~ 3
For the trans-structure, the dipole is around 36. The standard deviation ~ 3


How could GROMACS get the much lower standard deviation than what I
calculated?
Is there any specific rules while GROMACS decides the relative positions of
the counter ions to the rest of the molecules?
My calculation result is not very close to what GROMACS derived.
Am I doing correctly ?



For the cis-structure
Dipole moment from GROMACS
Average = 33.0312
Std. Dev. = 3.5144
Error = 0.0236
Dipole moment from my calculation = 45 to 75



For the trans-structure
Dipole moment from GROMACS
Average = 36.8470
Std. Dev. = 3.4917
Error = 0.0238
Dipole moment from my calculation = range from 35 to 77




Thank you
Lin

















dipole moment = 48.0 sum of q_i x_i
x_i is the atomic position.

I did not include the counter ion of the salt molecule in my calculation.
The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans.
Here "A" are a string of atoms, most of them are carbons.



For the cis-structure
Dipole moment from GROMACS
Average = 33.0312
Std. Dev. = 3.5144
Error = 0.0236
Dipole moment from my calculation = 55.8675



For the trans-structure
Dipole moment from GROMACS
Average = 36.8470
Std. Dev. = 3.4917
Error = 0.0238
Dipole moment from my calculation = 77.2346



Questions:
1. There is a huge discrepancy between my calculation results and GROMACS.
Or, the two results are within acceptable discrepancy ???

2. In the beginning, I suppose that the trans-structure has smaller dipole
moment than cis-structure. However, it seems to be the opposite conclusion
based on both GROMACS and my calculation. Is there something possible wrong
???

3. I get the partial charges from the Journal papers and the partial charges
are derived for the similar molecules as mine. Is that wrong?




Thank you
Lin
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Re: [gmx-users] Re: eigenvectors in readable format

[Ramachandran G]

In selecting the eigen vector i just want to make sure about my
consideration about the time frames. Should i need to consider the time
frame t= 0.0 or i need to start at non zero positive numbers? Thank you.
Rama

On Fri, Oct 15, 2010 at 11:00 PM, Tsjerk Wassenaar wrote:

> Hi Rama,
>
> You can convert the .trr file to readable .gro/.g96 with trjconv.
> Frames with positive times will correspond to eigenvectors; the time
> indicates the eigenvector index. Make sure not to use any options like
> pbc/fitting :p
>
> Cheers,
>
> Tsjerk
>
> On Sat, Oct 16, 2010 at 7:00 AM, Ramachandran G  wrote:
> > Hi,
> > Can anyone help to get the eigen vector in ascii format. I have with me
> the
> > trajectory file 'eigenvec.trr'.
> >
> > On using g_covar_d, i got the the ascii format file 'covar.dat'  and it
> has
> > covariance matrix of 3(NxN) number. But i am not interested in that.
> >
> > I am interested in getting the ascii(readable) format of eigenvector and
> > hessian.mtx .
> > Your help is highly appreciated. Thank you.
> >
> > with regards,
> > Rama
> >
> > On Fri, Oct 15, 2010 at 2:29 PM, Ramachandran G 
> wrote:
> >>
> >> Hi gmx users:
> >> I did normal mode analysis and got the hessian.mtx . Using the
> command
> >> g_nmeig_d on the hessian.mtx
> >> i got the eigenfreq.xvg, eigenval.xvg, eigenvec.trr.
> >>
> >> I need the complete eigenvector in the readable format. How i can get
> it?
> >> Thank you.
> >>
> >> with regards,
> >> Rama
> >>
> >> --
> >> Postdoctoral Research Scholar,
> >> Department of Chemistry,
> >> University of Nevada, Reno.
> >
> >
> >
> >
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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-- 
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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[gmx-users] rlist and rcoulomb

[Swarnendu Tripathi]

Dear gromacs users,

In section 4.6.3 of gromacs 4 manual it says ``... the interactions between
pairs that do not fall within rlist but do fall within max(rcoulomb,rvdw)
are computed during neighbor search (NS), and the forces and energy are
stored separately, and added to short-range forces at every time step
between successive NS.''

Now I find that if I use rlist (= rvdw) = rcoulomb then I only have Coulomb
(SR) values in the md.log file but if I use rlist (= rvdw) < rcoulomb then I
get both Coulomb (SR) and Coulomb (LR) values in the md.log. In both cases I
have assigned vdwtype=user and also rcoulomb=user for a tabulated potential
that I use.

Now, my question is how in the second case when rlist < rcoulomb I am
getting the Coulomb (LR) values in md.log? Particularly, I want to know how
the Coulomb (LR) is calculated? Is it calculated in the same way as Coulomb
(SR) and simply denoted as  Coulomb (LR), since rlist < rcoulomb? Or, in
this case it is suggested that I should always use rlist=rcoulomb.

Any suggestion is appreciated and thanks in advance.

-Swarnendu
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Re: [gmx-users] rlist and rcoulomb

[Justin A. Lemkul]

Swarnendu Tripathi wrote:

Dear gromacs users,

In section 4.6.3 of gromacs 4 manual it says ``... the interactions 
between pairs that do not fall within rlist but do fall within 
max(rcoulomb,rvdw) are computed during neighbor search (NS), and the 
forces and energy are stored separately, and added to short-range forces 
at every time step between successive NS.''


Now I find that if I use rlist (= rvdw) = rcoulomb then I only have 
Coulomb (SR) values in the md.log file but if I use rlist (= rvdw) < 
rcoulomb then I get both Coulomb (SR) and Coulomb (LR) values in the 
md.log. In both cases I have assigned vdwtype=user and also 
rcoulomb=user for a tabulated potential that I use. 

Now, my question is how in the second case when rlist < rcoulomb I am 
getting the Coulomb (LR) values in md.log? Particularly, I want to know 


You have twin-range interactions.  Some interactions do not occur within rlist, 
but occur within rcoulomb, which is beyond rlist.  This is exactly the case 
stated in the manual.  If rlist = rvdw, then max(rvdw,rcoulomb) finds that 
rcoulomb is larger than rvdw and thus defines the outer bound of the twin-range 
setup.


how the Coulomb (LR) is calculated? Is it calculated in the same way as 
Coulomb (SR) and simply denoted as  Coulomb (LR), since rlist < 


Probably in the same was as Coulomb (SR), but with the frequency described in 
the manual.


rcoulomb? Or, in this case it is suggested that I should always use 
rlist=rcoulomb.




Using rlist=rcoulomb is fairly common for many force fields, but whether or not 
this is required for your model is up to you.


-Justin


Any suggestion is appreciated and thanks in advance.

-Swarnendu



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] GPU slower than I7

[Roland Schulz]

On Thu, Oct 21, 2010 at 3:18 PM, Renato Freitas  wrote:

> Hi gromacs users,
>
> I have installed the lastest version of gromacs (4.5.1) in an i7 980X
> (6 cores or 12 with HT on; 3.3 GHz) with 12GB of RAM and compiled its
> mpi version. Also I compiled the GPU-accelerated
> version of gromacs. Then I did a  2 ns simulation using a small system
> (11042 atoms)  to compare the performance of mdrun-gpu vs mdrun_mpi.
> The results that I got are bellow:
>
> 
> My *.mdp is:
>
> constraints =  all-bonds
> integrator  =  md
> dt  =  0.002; ps !
> nsteps  =  100  ; total 2000 ps.
> nstlist =  10
> ns_type =  grid
> coulombtype= PME
> rvdw= 0.9
> rlist   = 0.9
> rcoulomb= 0.9
> fourierspacing  = 0.10
> pme_order   = 4
> ewald_rtol  = 1e-5
> vdwtype =  cut-off
> pbc =  xyz
> epsilon_rf=  0
> comm_mode   =  linear
> nstxout =  1000
> nstvout =  0
> nstfout =  0
> nstxtcout   =  1000
> nstlog  =  1000
> nstenergy   =  1000
> ; Berendsen temperature coupling is on in four groups
> tcoupl  = berendsen
> tc-grps = system
> tau-t   = 0.1
> ref-t   = 298
> ; Pressure coupling is on
> Pcoupl = berendsen
> pcoupltype = isotropic
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 298 K.
> gen_vel = no
>
> 
> RUNNING GROMACS ON GPU
>
> mdrun-gpu -s topol.tpr -v > & out &
>
> Here is a part of the md.log:
>
> Started mdrun on node 0 Wed Oct 20 09:52:09 2010
> .
> .
> .
> R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>
>  Computing: Nodes   Number  G-CyclesSeconds %
>
> --
>  Write traj.1   1021106.075 31.7
>  0.2
>  Rest   1   64125.577   19178.6
> 99.8
>
> --
>  Total  1   64231.652   19210.3 100.0
>
> --
>
>NODE (s)Real (s)(%)
>   Time:6381.84019210.349   33.2
>   1h46:21
>(Mnbf/s)   (MFlops) (ns/day)(hour/ns)
> Performance:0.000   0.001   27.077  0.886
>
> Finished mdrun on node 0 Wed Oct 20 15:12:19 2010
>
> 
> RUNNING GROMACS ON MPI
>
> mpirun -np 6 mdrun_mpi -s topol.tpr -npme 3 -v > & out &
>
> Here is a part of the md.log:
>
> Started mdrun on node 0 Wed Oct 20 18:30:52 2010
>
> R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>
>  Computing: Nodes   Number  G-CyclesSeconds %
>
> --
>  Domain decomp. 3  11 1452.166  434.7
> 0.6
>  DD comm. load  3  100010.745  0.2
>   0.0
>  Send X to PME 3  101249.003   74.5
>  0.1
>  Comm. coord.   3  101   637.329190.8
>  0.3
>  Neighbor search3  11 8738.669  2616.0
> 3.5
>  Force   3  101   99210.202
> 29699.239.2
>  Wait + Comm. F   3  101   3361.591   1006.3
>   1.3
>  PME mesh   3  101   66189.554 19814.2
>   26.2
>  Wait + Comm. X/F3  60294.513 8049.5  23.8
>  Wait + Recv. PME F 3  101801.897240.1
>   0.3
>  Write traj. 3  1015 33.464
>  10.0 0.0
>  Update 3  1013295.820
> 986.6  1.3
>  Constraints  3  101 6317.568
> 1891.2  2.5
>  Comm. energies   3  12  70.784  21.2
>   0.0
>  Rest3  2314.844
>693.0   0.9
>
> --
>  Total6  252968.14875727.5
> 100.0
>
> --
>
> --
>  PME redist. X/F

[gmx-users] problem with energy groups and mdrun -rerun option

[jagannath mondal]

Hi,  I have  used gromacs 4.0.7 to do  MD simulation of two solutes A & B in 
water ( solvent) . Initially, I had set "energy groups = system " and used 
mdrun to do the simulation.
Now,I wanted to get the potential energy contribution from due to interaction 
of  A-A, B-B,A-B A-solvent, B-solvent, solvent-solvent.For that I followed some 
discussions in mailing list regarding using mdrun -rerun option:This is what I 
did:I used make_ndx and created 3 groups: A, B and solvent.  Now, I modified 
the  grompp.mdp file so that I have now   energy groups = A B solvent   
Then I used grompp -c conf -f grompp -n index -o topol
Then I used mdrun -s -rerun traj_old.xtc 
( here traj_old.xtc is the old xtc file I obtained during the original mdrun)
But, now, after using this -rerun option , if I try to use the g_energy on the  
resulting ener.edr file to obtain the individual potential energy of 
interaction for A-A, B-B , A-B, A-solventI get following output 

Here is the output from g_energy -f ener.edr :
Select the terms you want from the following list byselecting either (part of) 
the name or the number or a combination.End your selection with an empty line 
or a 
zero.---  1  
Bond             2  Angle            3  U-B              4  Ryckaert-Bell.  5  
Improper-Dih.    6  LJ-14            7  Coulomb-14       8  LJ-(SR)     9  
Coulomb-(SR)    10  Coul.-recip.    11  Potential       12  Kinetic-En.    13  
Total-Energy    14  Conserved-En.   15  Temperature     16  Pressure-(bar) 17  
Cons.-rmsd-()   18  Vir-XX          19  Vir-XY          20  Vir-XZ         21  
Vir-YX          22  Vir-YY          23  Vir-YZ          24  Vir-ZX         25  
Vir-ZY          26  Vir-ZZ          27  Pres-XX-(bar)   28  Pres-XY-(bar)  29  
Pres-XZ-(bar)   30  Pres-YX-(bar)   31
  Pres-YY-(bar)   32  Pres-YZ-(bar)  33  Pres-ZX-(bar)   34  Pres-ZY-(bar)   35 
 Pres-ZZ-(bar)   36  #Surf*SurfTen  37  Mu-X            38  Mu-Y            39  
Mu-Z            40  Coul-SR:A-A    41  LJ-SR:A-A       42  Coul-14:A-A     43  
LJ-14:A-A       44  Coul-SR:A-B    45  LJ-SR:A-B                           46  
Coul-14:A-B                        47  LJ-14:A-B                           48  
Coul-SR:A-Solvent                  49  LJ-SR:A-Solvent                     50  
Coul-14:A-Solvent                  51  LJ-14:A-Solvent                     52  
Coul-SR:B-B                        53  LJ-SR:B-B                           54  
Coul-14:B-B                        55  LJ-14:B-B                           56  
Coul-SR:B-Solvent                  57
  LJ-SR:B-Solvent                     58  Coul-14:B-Solvent                  59 
 LJ-14:B-Solvent                     60  Coul-SR:Solvent-Solvent            61  
LJ-SR:Solvent-Solvent               62  Coul-14:Solvent-Solvent            63  
LJ-14:Solvent-Solvent               64  T-System                           65  
Xi-System
It provides me contribution from each of the energy groups on nonbonding terms: 
LJ(SR),Coulomb(SR),Coulomb(14),LJ(14) .  But, it does NOT provide me their 
contribution to Bonding term( i.e bond,angle, U-B,RB,improper-Dih) !!  As a 
result, I am a not sure how to get the net potential energy from each of the 3 
energy groups. Am I doing something wrong ? Do I need to use any other 
utilities ? Any help will be useful. 
Jagannath


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Re: [gmx-users] problem with energy groups and mdrun -rerun option

[Justin A. Lemkul]

jagannath mondal wrote:

Hi,
  I have  used gromacs 4.0.7 to do  MD simulation of two solutes A & B 
in water ( solvent) . 
Initially, I had set "energy groups = system " and used mdrun to do the 
simulation.


Now,I wanted to get the potential energy contribution from due to 
interaction of  A-A, B-B,A-B A-solvent, B-solvent, solvent-solvent.
For that I followed some discussions in mailing list regarding using 
mdrun -rerun option:

This is what I did:
I used make_ndx and created 3 groups: A, B and solvent.  
Now, I modified the  grompp.mdp file so that I have now 
  energy groups = A B solvent   


Then I used grompp -c conf -f grompp -n index -o topol

Then I used mdrun -s -rerun traj_old.xtc 

( here traj_old.xtc is the old xtc file I obtained during the original 
mdrun)


But, now, after using this -rerun option , if I try to use the g_energy 
on the  resulting ener.edr file to obtain the individual potential 
energy of interaction for A-A, B-B , A-B, A-solvent
I get following output 



Here is the output from g_energy -f ener.edr :

Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
---
  1  Bond 2  Angle3  U-B  4 
 Ryckaert-Bell.
  5  Improper-Dih.6  LJ-147  Coulomb-14   8  LJ-(SR) 
  
  9  Coulomb-(SR)10  Coul.-recip.11  Potential   12 
 Kinetic-En.   
 13  Total-Energy14  Conserved-En.   15  Temperature 16 
 Pressure-(bar)
 17  Cons.-rmsd-()   18  Vir-XX  19  Vir-XY  20  Vir-XZ 
   
 21  Vir-YX  22  Vir-YY  23  Vir-YZ  24  Vir-ZX 
   
 25  Vir-ZY  26  Vir-ZZ  27  Pres-XX-(bar)   28 
 Pres-XY-(bar) 
 29  Pres-XZ-(bar)   30  Pres-YX-(bar)   31  Pres-YY-(bar)   32 
 Pres-YZ-(bar) 
 33  Pres-ZX-(bar)   34  Pres-ZY-(bar)   35  Pres-ZZ-(bar)   36 
 #Surf*SurfTen 
 37  Mu-X38  Mu-Y39  Mu-Z40 
 Coul-SR:A-A   
 41  LJ-SR:A-A   42  Coul-14:A-A 43  LJ-14:A-A   44 
 Coul-SR:A-B   
 45  LJ-SR:A-B   46  Coul-14:A-B 
  
 47  LJ-14:A-B   48  Coul-SR:A-Solvent   
  
 49  LJ-SR:A-Solvent 50  Coul-14:A-Solvent   
  
 51  LJ-14:A-Solvent 52  Coul-SR:B-B 
  
 53  LJ-SR:B-B   54  Coul-14:B-B 
  
 55  LJ-14:B-B   56  Coul-SR:B-Solvent   
  
 57  LJ-SR:B-Solvent 58  Coul-14:B-Solvent   
  
 59  LJ-14:B-Solvent 60  Coul-SR:Solvent-Solvent 
  
 61  LJ-SR:Solvent-Solvent   62  Coul-14:Solvent-Solvent 
  
 63  LJ-14:Solvent-Solvent   64  T-System   
   
 65  Xi-System


It provides me contribution from each of the energy groups on nonbonding 
terms: LJ(SR),Coulomb(SR),Coulomb(14),LJ(14) .  But, it does NOT provide 
me their contribution to Bonding term( i.e bond,angle, 
U-B,RB,improper-Dih) !!  
As a result, I am a not sure how to get the net potential energy from 
each of the 3 energy groups. Am I doing something wrong ? Do I need to 
use any other utilities ?


Using energygrps only allows you to decompose nonbonded interactions.  You 
cannot decompose bonded interactions, potential, kinetic energy, etc.


-Justin

 Any help will be useful. 


Jagannath




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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Please search the archive at 
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Re: [gmx-users] problem with energy groups and mdrun -rerun option

[jagannath mondal]

Justin,Thanks  for your reply.  Then I wonder whether there is any other way 
out in gromacs to get the net interaction potential energy due to each of the 
components in a simulations. 
I am asking this, many times people report the potential energy contribution 
due to solvent-solvent interaction in a simulation containing solute( say 
peptide) and solvents and that are also being   done in gromacs. I wonder, for 
those cases, whether just adding the non-bonding interaction will be good 
enough ? or, there is any other way out ?Jagannath

--- On Fri, 22/10/10, Justin A. Lemkul  wrote:

From: Justin A. Lemkul 
Subject: Re: [gmx-users] problem with energy groups and mdrun -rerun option
To: "Discussion list for GROMACS users" 
Date: Friday, 22 October, 2010, 2:56 AM



jagannath mondal wrote:
> Hi,
>   I have  used gromacs 4.0.7 to do  MD simulation of two solutes A & B in 
>water ( solvent) . Initially, I had set "energy groups = system " and used 
>mdrun to do the simulation.
> 
> Now,I wanted to get the potential energy contribution from due to interaction 
> of  A-A, B-B,A-B A-solvent, B-solvent, solvent-solvent.
> For that I followed some discussions in mailing list regarding using mdrun 
> -rerun option:
> This is what I did:
> I used make_ndx and created 3 groups: A, B and solvent.  Now, I modified the  
> grompp.mdp file so that I have now   energy groups = A B solvent   
> Then I used grompp -c conf -f grompp -n index -o topol
> 
> Then I used mdrun -s -rerun traj_old.xtc 
> ( here traj_old.xtc is the old xtc file I obtained during the original mdrun)
> 
> But, now, after using this -rerun option , if I try to use the g_energy on 
> the  resulting ener.edr file to obtain the individual potential energy of 
> interaction for A-A, B-B , A-B, A-solvent
> I get following output 
> 
> Here is the output from g_energy -f ener.edr :
> 
> Select the terms you want from the following list by
> selecting either (part of) the name or the number or a combination.
> End your selection with an empty line or a zero.
> ---
>   1  Bond             2  Angle            3  U-B              4  
>Ryckaert-Bell.
>   5  Improper-Dih.    6  LJ-14            7  Coulomb-14       8  LJ-(SR)      
>   9  Coulomb-(SR)    10  Coul.-recip.    11  Potential       12  Kinetic-En.  
>  13  Total-Energy    14  Conserved-En.   15  Temperature     16  
>Pressure-(bar)
>  17  Cons.-rmsd-()   18  Vir-XX          19  Vir-XY          20  Vir-XZ       
>  21  Vir-YX          22  Vir-YY          23  Vir-YZ          24  Vir-ZX       
>  25  Vir-ZY          26  Vir-ZZ          27  Pres-XX-(bar)   28  
>Pres-XY-(bar)  29  Pres-XZ-(bar)   30  Pres-YX-(bar)   31  Pres-YY-(bar)   32  
>Pres-YZ-(bar)  33  Pres-ZX-(bar)   34  Pres-ZY-(bar)   35  Pres-ZZ-(bar)   36  
>#Surf*SurfTen  37  Mu-X            38  Mu-Y            39  Mu-Z            40  
>Coul-SR:A-A    41  LJ-SR:A-A       42  Coul-14:A-A     43  LJ-14:A-A       44  
>Coul-SR:A-B    45  LJ-SR:A-B                           46  Coul-14:A-B         
>               47  LJ-14:A-B                           48  Coul-SR:A-Solvent   
>               49  LJ-SR:A-Solvent                     50 
 Coul-14:A-Solvent                  51  LJ-14:A-Solvent                     52  
Coul-SR:B-B                        53  LJ-SR:B-B                           54  
Coul-14:B-B                        55  LJ-14:B-B                           56  
Coul-SR:B-Solvent                  57  LJ-SR:B-Solvent                     58  
Coul-14:B-Solvent                  59  LJ-14:B-Solvent                     60  
Coul-SR:Solvent-Solvent            61  LJ-SR:Solvent-Solvent               62  
Coul-14:Solvent-Solvent            63  LJ-14:Solvent-Solvent               64  
T-System                           65  Xi-System
> 
> It provides me contribution from each of the energy groups on nonbonding 
> terms: LJ(SR),Coulomb(SR),Coulomb(14),LJ(14) .  But, it does NOT provide me 
> their contribution to Bonding term( i.e bond,angle, U-B,RB,improper-Dih) !!  
> As a result, I am a not sure how to get the net potential energy from each of 
> the 3 energy groups. Am I doing something wrong ? Do I need to use any other 
> utilities ?

Using energygrps only allows you to decompose nonbonded interactions.  You 
cannot decompose bonded interactions, potential, kinetic energy, etc.

-Justin

>  Any help will be useful. 
> Jagannath
> 
> 

-- 

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


-- gmx-users mailing list    gmx-users@gromacs.org
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Please search the archive at 
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Please don't post (un)subscribe reque

Re: [gmx-users] problem with energy groups and mdrun -rerun option

[Justin A. Lemkul]

jagannath mondal wrote:

Justin,
Thanks  for your reply.  Then I wonder whether there is any other way 
out in gromacs to get the net interaction potential energy due to each 
of the components in a simulations. 

I am asking this, many times people report the potential energy 
contribution due to solvent-solvent interaction in a simulation 
containing solute( say peptide) and solvents and that are also being   
done in gromacs. I wonder, for those cases, whether just adding the 
non-bonding interaction will be good enough ? or, there is any other way 
out ?


Solvent-solvent interactions should describe just the nonbonded part of the 
potential, assuming they're referring to intermolecular interactions.  As it 
stands, these are the only interactions that can be decomposed in Gromacs 
without seriously overhauling the code.


-Justin


Jagannath

--- On *Fri, 22/10/10, Justin A. Lemkul //* wrote:


From: Justin A. Lemkul 
Subject: Re: [gmx-users] problem with energy groups and mdrun -rerun
option
To: "Discussion list for GROMACS users" 
Date: Friday, 22 October, 2010, 2:56 AM



jagannath mondal wrote:
 > Hi,
 >   I have  used gromacs 4.0.7 to do  MD simulation of two solutes
A & B in water ( solvent) . Initially, I had set "energy groups =
system " and used mdrun to do the simulation.
 >
 > Now,I wanted to get the potential energy contribution from due to
interaction of  A-A, B-B,A-B A-solvent, B-solvent, solvent-solvent.
 > For that I followed some discussions in mailing list regarding
using mdrun -rerun option:
 > This is what I did:
 > I used make_ndx and created 3 groups: A, B and solvent.  Now, I
modified the  grompp.mdp file so that I have now   energy groups = A
B solvent   
 > Then I used grompp -c conf -f grompp -n index -o topol

 >
 > Then I used mdrun -s -rerun traj_old.xtc
 > ( here traj_old.xtc is the old xtc file I obtained during the
original mdrun)
 >
 > But, now, after using this -rerun option , if I try to use the
g_energy on the  resulting ener.edr file to obtain the individual
potential energy of interaction for A-A, B-B , A-B, A-solvent
 > I get following output
 >
 > Here is the output from g_energy -f ener.edr :
 >
 > Select the terms you want from the following list by
 > selecting either (part of) the name or the number or a combination.
 > End your selection with an empty line or a zero.
 > ---
 >   1  Bond 2  Angle3  U-B  4 
Ryckaert-Bell.
 >   5  Improper-Dih.6  LJ-147  Coulomb-14   8 
LJ-(SR) 9  Coulomb-(SR)10  Coul.-recip.11 
Potential   12  Kinetic-En.13  Total-Energy14 
Conserved-En.   15  Temperature 16  Pressure-(bar)
 >  17  Cons.-rmsd-()   18  Vir-XX  19  Vir-XY  20 
Vir-XZ 21  Vir-YX  22  Vir-YY  23  Vir-YZ   
  24  Vir-ZX 25  Vir-ZY  26  Vir-ZZ  27 
Pres-XX-(bar)   28  Pres-XY-(bar)  29  Pres-XZ-(bar)   30 
Pres-YX-(bar)   31  Pres-YY-(bar)   32  Pres-YZ-(bar)  33 
Pres-ZX-(bar)   34  Pres-ZY-(bar)   35  Pres-ZZ-(bar)   36 
#Surf*SurfTen  37  Mu-X38  Mu-Y39  Mu-Z 
  40  Coul-SR:A-A41  LJ-SR:A-A   42  Coul-14:A-A 43 
LJ-14:A-A   44  Coul-SR:A-B45  LJ-SR:A-B   
   46  Coul-14:A-B47  LJ-14:A-B 
 48  Coul-SR:A-Solvent  49 
LJ-SR:A-Solvent 50  Coul-14:A-Solvent   
  51  LJ-14:A-Solvent 52  Coul-SR:B-B   
53  LJ-SR:B-B   54 
Coul-14:B-B55  LJ-14:B-B   
   56  Coul-SR:B-Solvent  57  LJ-SR:B-Solvent   
 58  Coul-14:B-Solvent  59 
LJ-14:B-Solvent 60  Coul-SR:Solvent-Solvent 
  61  LJ-SR:Solvent-Solvent   62 
Coul-14:Solvent-Solvent63  LJ-14:Solvent-Solvent   
   64  T-System   65  Xi-System

 >
 > It provides me contribution from each of the energy groups on
nonbonding terms: LJ(SR),Coulomb(SR),Coulomb(14),LJ(14) .  But, it
does NOT provide me their contribution to Bonding term( i.e
bond,angle, U-B,RB,improper-Dih) !!  As a result, I am a not sure
how to get the net potential energy from each of the 3 energy
groups. Am I doing something wrong ? Do I need to use any other
utilities ?

Using energygrps only allows you to decompose nonbonded
interactions.  You cannot decompose bonded interactions, potential,
kinetic energy, etc.

-Justin

 >  Any help will be u

Re: [gmx-users] GPU slower than I7

[Renato Freitas]

Thanks Roland. I will do a newer test using the fourier spacing equal
to 0.11. However, about the performance of GPU versus CPU (mpi) let me
try to explain it better:

The simulation using gromacs with GPU started and finished:

Started mdrun on node 0 Wed Oct 20 09:52:09 2010
Finished mdrun on node 0 Wed Oct 20 15:12:19 2010

Total time = 320 min

The simulation using gromacs with mpi started and finished:

Started mdrun on node 0 Wed Oct 20 18:30:52 2010
Finished mdrun on node 0 Wed Oct 20 22:01:14 2010

Total time = 211 min

Based on this numbers, it was the CPU with mpi that was faster than
the GPU, by aproximately 106 min. But looking at the end of each
output I have:

GPU

 NODE (s)Real (s)(%)
Time:6381.84019210.34933.2
1h46:21
 (Mnbf/s)   (MFlops) (ns/day)(hour/ns)
Performance:0.000   0.001  27.077  0.886

MPI

 NODE (s) Real (s)(%)
Time:12621.257   12621.257   100.0
   3h30:21
  (Mnbf/s)  (GFlops) (ns/day)(hour/ns)
Performance: 388.633  28.77313.691 1.753


Looking abobe we can see that the gromacs prints in the output that
the simulation is faster when the GPU is used. But this is not the
reality. The truth is that simulation time with MPI was 106 min faster
thatn that with GPU. It seems correct to you? As I said before, I was
expecting that GPU should take a lower time than the 6 core MPI.

Thanks,

Renato






2010/10/21 Roland Schulz :
>
>
> On Thu, Oct 21, 2010 at 3:18 PM, Renato Freitas  wrote:
>>
>> Hi gromacs users,
>>
>> I have installed the lastest version of gromacs (4.5.1) in an i7 980X
>> (6 cores or 12 with HT on; 3.3 GHz) with 12GB of RAM and compiled its
>> mpi version. Also I compiled the GPU-accelerated
>> version of gromacs. Then I did a  2 ns simulation using a small system
>> (11042 atoms)  to compare the performance of mdrun-gpu vs mdrun_mpi.
>> The results that I got are bellow:
>>
>> 
>> My *.mdp is:
>>
>> constraints         =  all-bonds
>> integrator          =  md
>> dt                  =  0.002    ; ps !
>> nsteps              =  100  ; total 2000 ps.
>> nstlist             =  10
>> ns_type             =  grid
>> coulombtype    = PME
>> rvdw                = 0.9
>> rlist               = 0.9
>> rcoulomb            = 0.9
>> fourierspacing      = 0.10
>> pme_order           = 4
>> ewald_rtol          = 1e-5
>> vdwtype             =  cut-off
>> pbc                 =  xyz
>> epsilon_rf    =  0
>> comm_mode           =  linear
>> nstxout             =  1000
>> nstvout             =  0
>> nstfout             =  0
>> nstxtcout           =  1000
>> nstlog              =  1000
>> nstenergy           =  1000
>> ; Berendsen temperature coupling is on in four groups
>> tcoupl              = berendsen
>> tc-grps             = system
>> tau-t               = 0.1
>> ref-t               = 298
>> ; Pressure coupling is on
>> Pcoupl = berendsen
>> pcoupltype = isotropic
>> tau_p = 0.5
>> compressibility = 4.5e-5
>> ref_p = 1.0
>> ; Generate velocites is on at 298 K.
>> gen_vel = no
>>
>> 
>> RUNNING GROMACS ON GPU
>>
>> mdrun-gpu -s topol.tpr -v > & out &
>>
>> Here is a part of the md.log:
>>
>> Started mdrun on node 0 Wed Oct 20 09:52:09 2010
>> .
>> .
>> .
>>     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>>
>>  Computing:     Nodes   Number          G-Cycles        Seconds     %
>>
>> --
>>  Write traj.    1               1021                    106.075 31.7
>>      0.2
>>  Rest                   1               64125.577               19178.6
>> 99.8
>>
>> --
>>  Total          1               64231.652               19210.3 100.0
>>
>> --
>>
>>                        NODE (s)                Real (s)                (%)
>>       Time:    6381.840                19210.349               33.2
>>                       1h46:21
>>                        (Mnbf/s)   (MFlops)     (ns/day)        (hour/ns)
>> Performance:    0.000   0.001   27.077  0.886
>>
>> Finished mdrun on node 0 Wed Oct 20 15:12:19 2010
>>
>> 
>> RUNNING GROMACS ON MPI
>>
>> mpirun -np 6 mdrun_mpi -s topol.tpr -npme 3 -v > & out &
>>
>> Here is a part of the md.log:
>>
>> Started mdrun on node 0 Wed Oct 20 18:30:52 2010
>>
>>     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>>
>>  Computing:             Nodes   Number  G-Cycles    Seconds             %
>>
>> --

[gmx-users] molecular surface area(MSA)?

[jagannath mondal]

Hi,  I was wondering whether gromacs can calculate a quantity called molecular 
surface area(MSA) which is different from solvent accessible surface area(SASA).
By definition, SASA of a molecule is the area of surface traced by center of a 
spherical water probe rolling on a vander wall surface of the given molecule. I 
think g_sas provides SASA.
But MSA is something different. It is the area generated by the part of the 
probe surface facing the given molecule. But, I am not sure whether gromacs can 
calculate it .
Jagannath

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RE: [gmx-users] molecular surface area(MSA)?

[Dallas Warren]

What you want then is a Connolly surface?

 

Which I gather is what GROMACS actually calculates,
http://www.mail-archive.com/gmx-users@gromacs.org/msg12518.html

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of jagannath mondal
Sent: Friday, 22 October 2010 9:19 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] molecular surface area(MSA)?

 

Hi,

  I was wondering whether gromacs can calculate a quantity called
molecular surface area(MSA) which is different from solvent accessible
surface area(SASA).

 

By definition, SASA of a molecule is the area of surface traced by
center of a spherical water probe rolling on a vander wall surface of
the given molecule. I think g_sas provides SASA.

 

But MSA is something different. It is the area generated by the part of
the probe surface facing the given molecule. But, I am not sure whether
gromacs can calculate it .

 

Jagannath

 

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Re: [gmx-users] GPU slower than I7

[Roland Schulz]

On Thu, Oct 21, 2010 at 5:53 PM, Renato Freitas  wrote:

> Thanks Roland. I will do a newer test using the fourier spacing equal
> to 0.11.

I'd also suggest to look at g_tune_pme and run with different rcoulomb,
fourier_spacing. As long as the ratio is the same you get the same accuracy.
And you should get better performance (especially on the GPU) for longer
cut-off and larger grid-spacing.


> However, about the performance of GPU versus CPU (mpi) let me
> try to explain it better:
>


> GPU
>
> NODE (s)Real (s)(%)
> Time:6381.84019210.34933.2
>1h46:21
> (Mnbf/s)   (MFlops) (ns/day)(hour/ns)
> Performance:0.000   0.001  27.077  0.886
>
> MPI
>
> NODE (s) Real (s)(%)
> Time:12621.257   12621.257   100.0
>   3h30:21
>  (Mnbf/s)  (GFlops) (ns/day)(hour/ns)
> Performance: 388.633  28.77313.691 1.753
>

Yes. Sorry I didn't realize that NODE time and  Real time is different. Did
you run the GPU calculation on a desktop machine which was also doing other
things at the time. This might explain it. As far as I know for a dedicated
machine not running any other programs NODE and Real time should be the
same.

Looking abobe we can see that the gromacs prints in the output that
> the simulation is faster when the GPU is used. But this is not the
> reality. The truth is that simulation time with MPI was 106 min faster
> thatn that with GPU. It seems correct to you? As I said before, I was
> expecting that GPU should take a lower time than the 6 core MPI.
>
 Well the exact time depends on a lot of factors. And you probably can speed
up both. But I would expect them to be both about similar fast.

Roland
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[gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

[Chih-Ying Lin]

Hi
When I issued the command g_dipole,
the dialog poped out and asked me to select a group.

1. system
2. protein

.

11. solvent
12. the rest of the salt-molecule except its counter ion
13. counter ions (CL-)


If I select #12, Gromacs will not consider counter ions to calculate the
dipole moment ???

Thank you
Lin
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Re: [gmx-users] problem with energy groups and mdrun -rerun option

[Mark Abraham]

On 22/10/2010 8:21 AM, jagannath mondal wrote:

Hi,
  I have  used gromacs 4.0.7 to do  MD simulation of two solutes A & B 
in water ( solvent) .
Initially, I had set "energy groups = system " and used mdrun to do 
the simulation.


Now,I wanted to get the potential energy contribution from due to 
interaction of  A-A, B-B,A-B A-solvent, B-solvent, solvent-solvent.
For that I followed some discussions in mailing list regarding using 
mdrun -rerun option:

This is what I did:
I used make_ndx and created 3 groups: A, B and solvent.
Now, I modified the  grompp.mdp file so that I have now
  energy groups = A B solvent

Then I used grompp -c conf -f grompp -n index -o topol

Then I used mdrun -s -rerun traj_old.xtc

( here traj_old.xtc is the old xtc file I obtained during the original 
mdrun)


But, now, after using this -rerun option , if I try to use the 
g_energy on the  resulting ener.edr file to obtain the individual 
potential energy of interaction for A-A, B-B , A-B, A-solvent

I get following output


Here is the output from g_energy -f ener.edr :

Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
---
  1  Bond 2  Angle3  U-B  4 
 Ryckaert-Bell.

  5  Improper-Dih.6  LJ-147  Coulomb-14   8  LJ-(SR)
  9  Coulomb-(SR)10  Coul.-recip.11  Potential   12 
 Kinetic-En.
 13  Total-Energy14  Conserved-En.   15  Temperature 16 
 Pressure-(bar)

 17  Cons.-rmsd-()   18  Vir-XX  19  Vir-XY  20  Vir-XZ
 21  Vir-YX  22  Vir-YY  23  Vir-YZ  24  Vir-ZX
 25  Vir-ZY  26  Vir-ZZ  27  Pres-XX-(bar)   28 
 Pres-XY-(bar)
 29  Pres-XZ-(bar)   30  Pres-YX-(bar)   31  Pres-YY-(bar)   32 
 Pres-YZ-(bar)
 33  Pres-ZX-(bar)   34  Pres-ZY-(bar)   35  Pres-ZZ-(bar)   36 
 #Surf*SurfTen
 37  Mu-X38  Mu-Y39  Mu-Z40 
 Coul-SR:A-A
 41  LJ-SR:A-A   42  Coul-14:A-A 43  LJ-14:A-A   44 
 Coul-SR:A-B

 45  LJ-SR:A-B   46  Coul-14:A-B
 47  LJ-14:A-B   48  Coul-SR:A-Solvent
 49  LJ-SR:A-Solvent 50  Coul-14:A-Solvent
 51  LJ-14:A-Solvent 52  Coul-SR:B-B
 53  LJ-SR:B-B   54  Coul-14:B-B
 55  LJ-14:B-B   56  Coul-SR:B-Solvent
 57  LJ-SR:B-Solvent 58  Coul-14:B-Solvent
 59  LJ-14:B-Solvent 60  Coul-SR:Solvent-Solvent
 61  LJ-SR:Solvent-Solvent   62  Coul-14:Solvent-Solvent
 63  LJ-14:Solvent-Solvent   64  T-System
 65  Xi-System

It provides me contribution from each of the energy groups on 
nonbonding terms: LJ(SR),Coulomb(SR),Coulomb(14),LJ(14) .  But, it 
does NOT provide me their contribution to Bonding term( i.e 
bond,angle, U-B,RB,improper-Dih) !!
As a result, I am a not sure how to get the net potential energy from 
each of the 3 energy groups. Am I doing something wrong ? Do I need to 
use any other utilities ?




Decomposing the bonded potential requires you to hack about in your .top 
for some more mdrun -rerun runs. For speed, in your .mdp file set 
rlist/rvdw/rcoulomb to some tiny value - this only affects non-bonded 
potential, which you don't care about this time. Then remove the bonded 
interactions from the .top for 2 of your groups, and a rerun will 
compute the bonded interactions of the third. Rinse, repeat.


Mark
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Re: [gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

[David van der Spoel]

On 2010-10-22 00.49, Chih-Ying Lin wrote:

Hi
When I issued the command g_dipole,
the dialog poped out and asked me to select a group.
1. system
2. protein

.

11. solvent
12. the rest of the salt-molecule except its counter ion
13. counter ions (CL-)
If I select #12, Gromacs will not consider counter ions to calculate the
dipole moment ???
Thank you
Lin

you should try to understand what is going on yourself rather than 
sending many email to the mailing list. Please read the source code of 
the program.


--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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