Re: [gmx-users] Temperature Histogram

[cuong nguyen]

Dear,

Thanks a lot for your suggestion Justin.
I have a box 3 3 20 and want to plot the temperature along the z axis. I
did the commands:
g_energy -f NVT_20ns.edr -s topol.top -o temp
g_analyze -f temp.xvg -dist temp.xvg

and got the results:
  281.9 0  282 0.000149997  282.1 0  282.2 0  282.3 0  282.4 0  282.5 0
282.6 0  282.7 0  282.8 0  282.9 0  283 0  283.1 0  283.2 0  283.3 0  283.4
0  283.5 0  283.6 0  283.7 0.000149997  283.8 0  283.9 0  284 0  284.1
0.000149997  284.2 0  284.3 0.000149997
 .

I supposed the first column should start from 0 to 20.
Please tell me what's wrong I am doing?

Best regards,

Cuong

On 8 November 2012 01:16, Justin Lemkul  wrote:

>
>
> On 11/7/12 11:42 AM, Samadashvili Nino wrote:
>
>> Hello,
>>
>>I would like to calculate temperature in my system along the axis.
>> Could you please tell me if there is a way to make a temperature histogram
>> with Gromacs?
>>
>>
> Use g_energy to extract temperatures from the .edr file, then g_analyze
> -dist on that .xvg file.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
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Re: [gmx-users] Re: Strange form of RDF curve

[Justin Lemkul]

On 11/19/12 10:04 PM, André Farias de Moura wrote:

from the statistical thermodynamics standpoint, rdf must be the same for
both choices of reference group, i.e.,solute-solvent and solvent-solute
must yield exactly the same rdf, the only difference being expected for the
cumulative numbers, which depend on the particles number density. The
reason why rdf's must be the same is the fact that rdf are connected to the
pmf between the particles, and the pmf do not depend upon the choice of
reference group, just on the reaction coordinate connecting the groups.



Doesn't this explanation assume that the system is homogeneous, or at least, 
that the solute (reference group) of interest exhaustively samples 
configurations within the solvent?  It's not intuitive to me why one would 
expect an Arg-water RDF to be the same as a Water-Arg RDF when the Arg residue 
is only part of a 582-residue protein, which means a considerable portion of the 
simulation unit cell contains neither the Arg of interest nor water, a fact that 
significantly impacts the binning as shown in the manual.  The actual g_rdf 
command is essential in this regard, as well, depending on how the RDF is being 
calculated.  One can produce wildly different results by changing only a a 
single element of the command.


-Justin

--


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


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Re: [gmx-users] Re: Strange form of RDF curve

[André Farias de Moura]

from the statistical thermodynamics standpoint, rdf must be the same for
both choices of reference group, i.e.,solute-solvent and solvent-solute
must yield exactly the same rdf, the only difference being expected for the
cumulative numbers, which depend on the particles number density. The
reason why rdf's must be the same is the fact that rdf are connected to the
pmf between the particles, and the pmf do not depend upon the choice of
reference group, just on the reaction coordinate connecting the groups.

cheers

Andre

On Mon, Nov 19, 2012 at 2:50 PM, shch406  wrote:

> >I would have chosen the groups in the opposite manner.  You're interested
> in
> the
> >presence of water around the chosen arginine residue, not the presence of
> >arginine around water, right?  Given this order of chosen groups, the RDF
> seems
> >to make sense (very low probability that arginine is close to all water
> >molecules), though it doesn't represent what you likely want.
>
> >-Justin
>
> Of coarse, I'm interested in the presence of water around the arginine.
> But I did reverse order of groups, i.e. I toke water as the "1 group" and
> arginine sige
> chain tip as the "reference group", however have obtained absolutely the
> same curve.
> May be there exist some peculiarity in using g_rdf dialog to select groups?
>
> -Igor
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/Strange-form-of-RDF-curve-tp5003001p5003088.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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>
>


-- 
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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Re: [gmx-users] mpirun error

[Justin Lemkul]

On 11/19/12 12:09 PM, Parisa Rahmani wrote:

Dear gmx users

I have a problem with running parallel jobs on my Debian system(Openmpi
installed on it),
**Linux debian 3.2.0-1-amd64 #1 SMP , UTC 2012 x86_64 GNU/Linux**
I am using gmx 3.3.3, because of the *lambda dynamics* method which is
implemented in it.

AS I know ,in gmx 3.x, the number of processors supplied for the subsequent
mdrun needed to match the input file. but when i use **grompp -np 6 &
mpirun -np 6 mdrun** the following error appears :

ERROR : run input file md.tpr was made for 6 nodes,
while mdrun expected it to be for 1 nodes.

through search of mailing list i found similar problems, but non of
the solutions worked for my case.

wihtout -np option in grompp the error disappears, and then with each
of these commands

**

1)mpirun -np 6 mdrun -deffnm md

2)mpirun -np 6 mdrun -deffnm md -N 6

3)mpirun -np 6 mdrun -np 6 -deffnm md

4)mdrun -np 6 -s md -N 6


**it uses 6 processors(each one at nearly 100%), but the simulation
time is the same as for 1 processor.

I have no problem with parallel jobs on our cluster(gmx 3.3.3 &
openmpi), with following command:

**
grompp -np 6 -f ...
mpiexec mdrun ...(number of processors is specified in the bash file)
**
,
but i can't run it on my 6 core system.

Also, I have no problem with newer version of gmx (4.5.x), but i
should use this version, and Hope someone can help me.



Have you properly compiled an MPI-enabled mdrun?  The default executable name 
should be mdrun_mpi.  It should be linked against libmpi, so running ldd on the 
mdrun executable should tell you.


-Justin

--


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


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Re: [gmx-users] Re: Strange form of RDF curve

[Justin Lemkul]

On 11/19/12 11:50 AM, shch406 wrote:

I would have chosen the groups in the opposite manner.  You're interested in

the

presence of water around the chosen arginine residue, not the presence of
arginine around water, right?  Given this order of chosen groups, the RDF

seems

to make sense (very low probability that arginine is close to all water
molecules), though it doesn't represent what you likely want.



-Justin


Of coarse, I'm interested in the presence of water around the arginine.
But I did reverse order of groups, i.e. I toke water as the "1 group" and
arginine sige
chain tip as the "reference group", however have obtained absolutely the
same curve.
May be there exist some peculiarity in using g_rdf dialog to select groups?



I've never had an issue with similar commands.  Can you provide us with your 
full g_rdf command line?  Have you verified that the index group for the 
arginine residue is correct?  Can you provide a link to an image of the 
resulting RDF?


-Justin

--


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


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[gmx-users] REMD simulation

[Christopher Neale]

Xavier is right, except that you can also reduce the size of your system. You 
can take larger steps in temperature 
if you have fewer atoms. If you are using a  cubic system, you can move to a 
rhombic dodecahedron. 
Even constraining all bonds will help a bit here (vs. harmonic bonds). 
There are lots of papers on this topic.

To see why you don't get any exchanges, construct histograms of your potential 
energies and you will see
that they don't overlap. Also, it is inefficient to take evenly spaced 
temperatures. This is not your major problem,
but read a bit on exponentially spaced temperatures for REMD.

Chris.

-- original message --

Well either you use more replicas or you reduce the temperature  
range ...
There is no way around!

On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote:

> Dear All,
>
> i am trying to performed REMD simulations using Gromacs.
> My question is concerning the temperature distribution and the  
> number of replica.
> I need to run 24 replicas of my system with a temperature range of  
> 290-400 K. How can I select the temperatures values for each replica?
> I tried the server http://folding.bmc.uu.se/remd/index.php but for  
> my system it gives 50 replicas. If i try to take 24 evenly spaced  
> values from the obtained list of temperature then
> the replicas do not exchange at all.
> I am using Gromacs 4.5.5 and my system has 6862 water molecules and  
> 535 atoms for the solute.
>
> Thanks in advanced
> Kenny
>
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Re: [gmx-users] gmx 4.6: incompatible gpu device

[Justin Lemkul]

On 11/19/12 2:44 PM, Oliver Mirus wrote:

Hi,

I've downloaded Gromacs 4.6:

git checkout --track -b release-4-6 origin/release-4-6

With '-msse4.1' added to CMAKE_C_FLAGS it finally compiled.

But a test run with 1 CPU & 1 GPU failed with the following message
before it started :
--
mdrun -deffnm gputest -gpu_id $gpulist

1 GPU detected:
   #0: NVIDIA Tesla T10 Processor, compute cap.: 1.3, ECC:  no, stat:
incompatible

Fatal error:
Some of the requested GPUs do not exist, behave strangely, or are not
compatible:
 GPU #2: inexistent
--
I had Gromacs 4.5.5 with OpenMM 4.0 running on the same GPU cluster, but
only with the option "force-device=yes". Is there a similar option in
Gromacs 4.6?



The same option exists if one compiles with external OpenMM support (not 
default).  You would need to build the mdrun-openmm binary using GMX_OPENMM=ON 
when running cmake.  Note that native mdrun GPU support is different than using 
OpenMM.


-Justin

--


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


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[gmx-users] gmx 4.6: incompatible gpu device

[Oliver Mirus]

Hi,

I've downloaded Gromacs 4.6:

git checkout --track -b release-4-6 origin/release-4-6

With '-msse4.1' added to CMAKE_C_FLAGS it finally compiled.

But a test run with 1 CPU & 1 GPU failed with the following message
before it started :
--
mdrun -deffnm gputest -gpu_id $gpulist

1 GPU detected:
  #0: NVIDIA Tesla T10 Processor, compute cap.: 1.3, ECC:  no, stat:
incompatible

Fatal error:
Some of the requested GPUs do not exist, behave strangely, or are not
compatible:
GPU #2: inexistent
--
I had Gromacs 4.5.5 with OpenMM 4.0 running on the same GPU cluster, but
only with the option "force-device=yes". Is there a similar option in
Gromacs 4.6?

Thanks

Oliver
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Re: [gmx-users] which version it is

[Thomas Piggot]

Hi Stephane,

The confusion was my fault, I did not realise that there were newly 
developed CHARMM36 protein parameters (Justin kindly pointed this out). 
You were quite correct that the contribution only contains the update 
for the lipids.


Cheers

Tom

On 19/11/12 18:49, ABEL Stephane 175950 wrote:

Hi Thomas and Justin,

I agree with you, but I think that Albert asked if the GROMACS 4.5.4 version of 
the CHARMM36 force field files contain the newly  developed parameters for 
protein (also called CHARMM36) and described in

Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M., & 
MacKerell, A. D. (2012). Optimization of the additive CHARMM all-atom protein force 
field targeting improved sampling of the backbone φ, ψ and side-chain χ1 and χ2 
dihedral angles. Journal of Chemical Theory and Computation, 120718184839007. 
doi:10.1021/ct300400x

I said no

Sorry if it was not clear in my previous message

Stephane


--

Message: 1
Date: Mon, 19 Nov 2012 16:14:48 +
From: ABEL Stephane 175950 
Subject: [gmx-users] which version it is
To: "gmx-users@gromacs.org" 
Message-ID:
 <3e39b768bb199548ab18f7289e7534af02d1c...@exdag0-b0.intra.cea.fr>
Content-Type: text/plain; charset="us-ascii"

Hi,

Probably the "CHARMM27_protein+Charmm36_lipids" version. AFAIK, the second 
version was not already converted in GROMACS format.

Stephane

---

hello:

   I found a charmm36.tar.gz in Gromacs website


   GROMACS 4.5.4 version of the CHARMM36 force field files. These updated
CHARMM lipids allow the all-atom simulations of membrane and
membrane-protein systems without the use of surface tension. Check out
the forcefield.doc for more information regarding these files
  71.65 kB15:42, 25 Sep 2012TomPiggot


I am just wondering, is the the one with
CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids?

thank you very much
best
Albert


--

Message: 3
Date: Mon, 19 Nov 2012 16:28:28 +
From: Thomas Piggot 
Subject: Re: [gmx-users] which version it is
To: Discussion list for GROMACS users 
Message-ID: <50aa5e2c.4000...@soton.ac.uk>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed

Hi,

As I understand it, the current and most up to date CHARMM protein force
field (as included in both the charmm27 and charmm36 force field
directories) is the CHARMM22 protein force field with the CMAP
correction. In other words there would be no difference between the two
options originally mentioned.

Cheers

Tom

ABEL Stephane 175950 wrote:

Hi,

Probably the "CHARMM27_protein+Charmm36_lipids" version. AFAIK, the second 
version was not already converted in GROMACS format.

Stephane

---

hello:

   I found a charmm36.tar.gz in Gromacs website


   GROMACS 4.5.4 version of the CHARMM36 force field files. These updated
CHARMM lipids allow the all-atom simulations of membrane and
membrane-protein systems without the use of surface tension. Check out
the forcefield.doc for more information regarding these files
  71.65 kB15:42, 25 Sep 2012TomPiggot


I am just wondering, is the the one with
CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids?

thank you very much
best
Albert

--
Dr Thomas Piggot
University of Southampton, UK.


--

Message: 4
Date: Mon, 19 Nov 2012 11:34:28 -0500
From: Justin Lemkul 
Subject: Re: [gmx-users] which version it is
To: Discussion list for GROMACS users 
Message-ID: <50aa5f94.6090...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 11/19/12 11:28 AM, Thomas Piggot wrote:

Hi,

As I understand it, the current and most up to date CHARMM protein force field
(as included in both the charmm27 and charmm36 force field directories) is the
CHARMM22 protein force field with the CMAP correction. In other words there
would be no difference between the two options originally mentioned.


There is indeed a CHARMM36 protein force field that is distinct from the one
included in CHARMM27 (which is, as you say, CHARMM22 + CMAP).

http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=30472

-Justin

--


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




--

Message: 5
Date: Mon, 19 Nov 2012 16:48:27 +
From: Thomas Piggot 
Subject: Re: [gmx-users] which version it is
To: Discussion list for GROMACS users 
Message-ID: <50aa62db.8010...@soton.ac.uk>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed

I must have missed that one, thanks for the link!

So, to confirm, the protein force field in the CHARMM36 f

[gmx-users] which version it is

[ABEL Stephane 175950]

Hi Thomas and Justin, 

I agree with you, but I think that Albert asked if the GROMACS 4.5.4 version of 
the CHARMM36 force field files contain the newly  developed parameters for 
protein (also called CHARMM36) and described in 

Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M., & 
MacKerell, A. D. (2012). Optimization of the additive CHARMM all-atom protein 
force field targeting improved sampling of the backbone φ, ψ and side-chain χ1 
and χ2 dihedral angles. Journal of Chemical Theory and Computation, 
120718184839007. doi:10.1021/ct300400x

I said no

Sorry if it was not clear in my previous message

Stephane


--

Message: 1
Date: Mon, 19 Nov 2012 16:14:48 +
From: ABEL Stephane 175950 
Subject: [gmx-users] which version it is
To: "gmx-users@gromacs.org" 
Message-ID:
<3e39b768bb199548ab18f7289e7534af02d1c...@exdag0-b0.intra.cea.fr>
Content-Type: text/plain; charset="us-ascii"

Hi,

Probably the "CHARMM27_protein+Charmm36_lipids" version. AFAIK, the second 
version was not already converted in GROMACS format.

Stephane

---

hello:

  I found a charmm36.tar.gz in Gromacs website


  GROMACS 4.5.4 version of the CHARMM36 force field files. These updated
CHARMM lipids allow the all-atom simulations of membrane and
membrane-protein systems without the use of surface tension. Check out
the forcefield.doc for more information regarding these files
 71.65 kB15:42, 25 Sep 2012TomPiggot


I am just wondering, is the the one with
CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids?

thank you very much
best
Albert


--

Message: 3
Date: Mon, 19 Nov 2012 16:28:28 +
From: Thomas Piggot 
Subject: Re: [gmx-users] which version it is
To: Discussion list for GROMACS users 
Message-ID: <50aa5e2c.4000...@soton.ac.uk>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed

Hi,

As I understand it, the current and most up to date CHARMM protein force
field (as included in both the charmm27 and charmm36 force field
directories) is the CHARMM22 protein force field with the CMAP
correction. In other words there would be no difference between the two
options originally mentioned.

Cheers

Tom

ABEL Stephane 175950 wrote:
> Hi,
>
> Probably the "CHARMM27_protein+Charmm36_lipids" version. AFAIK, the second 
> version was not already converted in GROMACS format.
>
> Stephane
>
> ---
>
> hello:
>
>   I found a charmm36.tar.gz in Gromacs website
>
>
>   GROMACS 4.5.4 version of the CHARMM36 force field files. These updated
> CHARMM lipids allow the all-atom simulations of membrane and
> membrane-protein systems without the use of surface tension. Check out
> the forcefield.doc for more information regarding these files
>  71.65 kB15:42, 25 Sep 2012TomPiggot
>
>
> I am just wondering, is the the one with
> CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids?
>
> thank you very much
> best
> Albert

--
Dr Thomas Piggot
University of Southampton, UK.


--

Message: 4
Date: Mon, 19 Nov 2012 11:34:28 -0500
From: Justin Lemkul 
Subject: Re: [gmx-users] which version it is
To: Discussion list for GROMACS users 
Message-ID: <50aa5f94.6090...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 11/19/12 11:28 AM, Thomas Piggot wrote:
> Hi,
>
> As I understand it, the current and most up to date CHARMM protein force field
> (as included in both the charmm27 and charmm36 force field directories) is the
> CHARMM22 protein force field with the CMAP correction. In other words there
> would be no difference between the two options originally mentioned.
>

There is indeed a CHARMM36 protein force field that is distinct from the one
included in CHARMM27 (which is, as you say, CHARMM22 + CMAP).

http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=30472

-Justin

--


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




--

Message: 5
Date: Mon, 19 Nov 2012 16:48:27 +
From: Thomas Piggot 
Subject: Re: [gmx-users] which version it is
To: Discussion list for GROMACS users 
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I must have missed that one, thanks for the link!

So, to confirm, the protein force field in the CHARMM36 force field
contribution is the CHARMM22 protein force field with the CMAP
correction. The contribution is just for the updated CHARMM36 lipids.

Cheers

Tom

Justin Lemkul wrote:
>
>
> On 11/19/12 11:28 AM, Thomas Piggot wrote:
>> Hi,
>>
>> As I understand i

Re: [gmx-users] which version it is

[Albert]

On 11/19/2012 05:48 PM, Thomas Piggot wrote:

I must have missed that one, thanks for the link!

So, to confirm, the protein force field in the CHARMM36 force field 
contribution is the CHARMM22 protein force field with the CMAP 
correction. The contribution is just for the updated CHARMM36 lipids.


Cheers

Tom


yes, they also claimed that this update version can prevent SF 
degradation during the micro second long time simulation. It seems 
to be promising

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Re: [gmx-users] GPU warnings

[Szilárd Páll]

On Mon, Nov 19, 2012 at 4:09 PM, Thomas Evangelidis wrote:

> Hi Szilárd,
>
> I compiled with the Intel compilers, not gcc. In case I am missing
> something, these are the versions I have:
>

Indeed, I see it now in the log file. Let me try with icc 13 and will get
back to you.

>
> glibc.i6862.15-57.fc17
> @updates
> glibc.x86_64  2.15-57.fc17
> @updates
> glibc-common.x86_64   2.15-57.fc17
> @updates
> glibc-devel.i686  2.15-57.fc17
> @updates
> glibc-devel.x86_642.15-57.fc17
> @updates
> glibc-headers.x86_64  2.15-57.fc17   @updates
>
> gcc.x86_644.7.2-2.fc17
> @updates
> gcc-c++.x86_644.7.2-2.fc17
> @updates
> gcc-gfortran.x86_64   4.7.2-2.fc17
> @updates
> libgcc.i686   4.7.2-2.fc17
> @updates
> libgcc.x86_64 4.7.2-2.fc17   @updates
>
>
> Thomas
>
>
>
> On 19 November 2012 16:57, Szilárd Páll  wrote:
>
> > Thomas & Albert,
> >
> > We are unable to reproduce the issue on FC 17 with glibc 2.15-58 and gcc
> > 4.7.2.
> >
> > Please try to update your packages (you should have updates available for
> > glibc), try recompiling with the latest 4.6 code and report back whether
> > you succeed.
> >
> > Cheers,
> >
> > --
> > Szilárd
> >
> >
> > On Fri, Nov 16, 2012 at 4:31 PM, Szilárd Páll  > >wrote:
> >
> > > Hi Albert,
> > >
> > > Apologies for hijacking your thread. Do you happen to have Fedora 17 as
> > > well?
> > >
> > > --
> > > Szilárd
> > >
> > >
> > >
> > > On Sun, Nov 4, 2012 at 10:55 AM, Albert  wrote:
> > >
> > >> hello:
> > >>
> > >>  I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2
> x
> > >> 1344 CUDA cores), and I got the following warnings:
> > >>
> > >> thank you very much.
> > >>
> > >> ---**messages--**
> > >> -
> > >>
> > >> WARNING: On node 0: oversubscribing the available 0 logical CPU cores
> > per
> > >> node with 2 MPI processes.
> > >>  This will cause considerable performance loss!
> > >>
> > >> 2 GPUs detected on host boreas:
> > >>   #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> > >> compatible
> > >>   #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> > >> compatible
> > >>
> > >> 2 GPUs auto-selected to be used for this run: #0, #1
> > >>
> > >> Using CUDA 8x8x8 non-bonded kernels
> > >> Making 1D domain decomposition 1 x 2 x 1
> > >>
> > >> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
> > >> We have just committed the new CPU detection code in this branch,
> > >> and will commit new SSE/AVX kernels in a few days. However, this
> > >> means that currently only the NxN kernels are accelerated!
> > >> In the mean time, you might want to avoid production runs in 4.6.
> > >>
> > >> --
> > >> gmx-users mailing listgmx-users@gromacs.org
> > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > >> * Please search the archive at http://www.gromacs.org/**
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> > >>
> > >
> > >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
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> >
>
>
>
> --
>
> ==
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tev...@pharm.uoa.gr
>
>   teva...@gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
> --
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Re: [gmx-users] REMD simulation

[XAvier Periole]

Well either you use more replicas or you reduce the temperature  
range ...

There is no way around!

On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote:


Dear All,

i am trying to performed REMD simulations using Gromacs.
My question is concerning the temperature distribution and the  
number of replica.
I need to run 24 replicas of my system with a temperature range of  
290-400 K. How can I select the temperatures values for each replica?
I tried the server http://folding.bmc.uu.se/remd/index.php but for  
my system it gives 50 replicas. If i try to take 24 evenly spaced  
values from the obtained list of temperature then

the replicas do not exchange at all.
I am using Gromacs 4.5.5 and my system has 6862 water molecules and  
535 atoms for the solute.


Thanks in advanced
Kenny

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[gmx-users] REMD simulation

[Kenny Bravo Rodriguez]

Dear All,

i am trying to performed REMD simulations using Gromacs.
My question is concerning the temperature distribution and the number of 
replica.
I need to run 24 replicas of my system with a temperature range of 
290-400 K. How can I select the temperatures values for each replica?
I tried the server http://folding.bmc.uu.se/remd/index.php but for my 
system it gives 50 replicas. If i try to take 24 evenly spaced values 
from the obtained list of temperature then

the replicas do not exchange at all.
I am using Gromacs 4.5.5 and my system has 6862 water molecules and 535 
atoms for the solute.


Thanks in advanced
Kenny

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[gmx-users] Re: Strange form of RDF curve

[shch406]

>I would have chosen the groups in the opposite manner.  You're interested in
the 
>presence of water around the chosen arginine residue, not the presence of 
>arginine around water, right?  Given this order of chosen groups, the RDF
seems 
>to make sense (very low probability that arginine is close to all water 
>molecules), though it doesn't represent what you likely want.

>-Justin

Of coarse, I'm interested in the presence of water around the arginine.
But I did reverse order of groups, i.e. I toke water as the "1 group" and
arginine sige
chain tip as the "reference group", however have obtained absolutely the
same curve.
May be there exist some peculiarity in using g_rdf dialog to select groups?

-Igor




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Re: [gmx-users] which version it is

[Thomas Piggot]

I must have missed that one, thanks for the link!

So, to confirm, the protein force field in the CHARMM36 force field 
contribution is the CHARMM22 protein force field with the CMAP 
correction. The contribution is just for the updated CHARMM36 lipids.


Cheers

Tom

Justin Lemkul wrote:



On 11/19/12 11:28 AM, Thomas Piggot wrote:

Hi,

As I understand it, the current and most up to date CHARMM protein 
force field
(as included in both the charmm27 and charmm36 force field 
directories) is the
CHARMM22 protein force field with the CMAP correction. In other words 
there

would be no difference between the two options originally mentioned.



There is indeed a CHARMM36 protein force field that is distinct from the 
one included in CHARMM27 (which is, as you say, CHARMM22 + CMAP).


http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=30472

-Justin



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University of Southampton, UK.
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Re: [gmx-users] which version it is

[Justin Lemkul]

On 11/19/12 11:28 AM, Thomas Piggot wrote:

Hi,

As I understand it, the current and most up to date CHARMM protein force field
(as included in both the charmm27 and charmm36 force field directories) is the
CHARMM22 protein force field with the CMAP correction. In other words there
would be no difference between the two options originally mentioned.



There is indeed a CHARMM36 protein force field that is distinct from the one 
included in CHARMM27 (which is, as you say, CHARMM22 + CMAP).


http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=30472

-Justin

--


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


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Re: [gmx-users] which version it is

[Thomas Piggot]

Hi,

As I understand it, the current and most up to date CHARMM protein force 
field (as included in both the charmm27 and charmm36 force field 
directories) is the CHARMM22 protein force field with the CMAP 
correction. In other words there would be no difference between the two 
options originally mentioned.


Cheers

Tom

ABEL Stephane 175950 wrote:
Hi, 

Probably the "CHARMM27_protein+Charmm36_lipids" version. AFAIK, the second version was not already converted in GROMACS format. 


Stephane

---

hello:

  I found a charmm36.tar.gz in Gromacs website


  GROMACS 4.5.4 version of the CHARMM36 force field files. These updated 
CHARMM lipids allow the all-atom simulations of membrane and 
membrane-protein systems without the use of surface tension. Check out 
the forcefield.doc for more information regarding these files

 71.65 kB15:42, 25 Sep 2012TomPiggot


I am just wondering, is the the one with 
CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids?


thank you very much
best
Albert


--
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University of Southampton, UK.
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[gmx-users] reaction field

[wmiranda]

Hello
I would like to perform a molecular simulation with the AMBER99SB FF ,
tip3p water model and reaction field for long range interactions. Which
value of epsilon_rf (The relative dielectric constant of the reaction
field) do I have to use?
Thanks
Williams



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[gmx-users] which version it is

[ABEL Stephane 175950]

Hi, 

Probably the "CHARMM27_protein+Charmm36_lipids" version. AFAIK, the second 
version was not already converted in GROMACS format. 

Stephane

---

hello:

  I found a charmm36.tar.gz in Gromacs website


  GROMACS 4.5.4 version of the CHARMM36 force field files. These updated 
CHARMM lipids allow the all-atom simulations of membrane and 
membrane-protein systems without the use of surface tension. Check out 
the forcefield.doc for more information regarding these files
 71.65 kB15:42, 25 Sep 2012TomPiggot


I am just wondering, is the the one with 
CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids?

thank you very much
best
Albert
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Re: [gmx-users] min + capped peptide

[Justin Lemkul]

On 11/19/12 10:54 AM, Bahar Mehrpuyan wrote:

thanks Justin for the reply
sorry , I asked my question in a wrong way,
I mean should I do geometry optimization for that capped peptide(protein)?(with
mm force field and steepest descent algorithm)



You should do an energy minimization with whatever force field you intend to use 
for the simulations.


-Justin




*From:* Justin Lemkul 
*To:* Bahar Mehrpuyan ; Discussion list for GROMACS
users 
*Sent:* Monday, November 19, 2012 6:55 PM
*Subject:* Re: [gmx-users] min + capped peptide



On 11/19/12 5:30 AM, Bahar Mehrpuyan wrote:
 > Hi gmx users
 >
 > I want to cap my peptide (adding ACE & NAC) with Avogadro package , my
question is , should I minimize the capped peptide with forcefields(molecular
mechanics) available in avogadro, then use it in the simulation? or just
simulation procedures (minimization and equilibration) is sufficient for
minimizing the peptide structure.
 >

This question does not make sense to me.  All sensible workflows involve
minimization and equilibration steps, which are distinct.  Minimization is a
non-dynamical process that seeks a stable energy minimum to begin the
simulation.  Equilibration prepares the system for data collection by optimizing
solvent around the solute (and maybe other factors, depending on what's in the
system) and establishing a stable thermodynamic ensemble.

-Justin

-- 

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






--


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


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Re: [gmx-users] min + capped peptide

[Bahar Mehrpuyan]

thanks Justin for the reply
sorry , I asked my question in a wrong way,
I mean should I do geometry optimization for that capped peptide(protein)?(with 
mm force field and steepest descent algorithm)





 From: Justin Lemkul 
To: Bahar Mehrpuyan ; Discussion list for GROMACS 
users  
Sent: Monday, November 19, 2012 6:55 PM
Subject: Re: [gmx-users] min + capped peptide
 


On 11/19/12 5:30 AM, Bahar Mehrpuyan wrote:
> Hi gmx users
> 
> I want to cap my peptide (adding ACE & NAC) with Avogadro package , my 
> question is , should I minimize the capped peptide with forcefields(molecular 
> mechanics) available in avogadro, then use it in the simulation? or just 
> simulation procedures (minimization and equilibration) is sufficient for 
> minimizing the peptide structure.
> 

This question does not make sense to me.  All sensible workflows involve 
minimization and equilibration steps, which are distinct.  Minimization is a 
non-dynamical process that seeks a stable energy minimum to begin the 
simulation.  Equilibration prepares the system for data collection by 
optimizing solvent around the solute (and maybe other factors, depending on 
what's in the system) and establishing a stable thermodynamic ensemble.

-Justin

-- 

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


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Re: [gmx-users] min + capped peptide

[Justin Lemkul]

On 11/19/12 5:30 AM, Bahar Mehrpuyan wrote:

Hi gmx users

I want to cap my peptide (adding ACE & NAC) with Avogadro package , my question 
is , should I minimize the capped peptide with forcefields(molecular mechanics) 
available in avogadro, then use it in the simulation? or just simulation procedures 
(minimization and equilibration) is sufficient for minimizing the peptide structure.



This question does not make sense to me.  All sensible workflows involve 
minimization and equilibration steps, which are distinct.  Minimization is a 
non-dynamical process that seeks a stable energy minimum to begin the 
simulation.  Equilibration prepares the system for data collection by optimizing 
solvent around the solute (and maybe other factors, depending on what's in the 
system) and establishing a stable thermodynamic ensemble.


-Justin

--


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


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Re: [gmx-users] GPU warnings

[Thomas Evangelidis]

Hi Szilárd,

I compiled with the Intel compilers, not gcc. In case I am missing
something, these are the versions I have:

glibc.i6862.15-57.fc17
@updates
glibc.x86_64  2.15-57.fc17
@updates
glibc-common.x86_64   2.15-57.fc17
@updates
glibc-devel.i686  2.15-57.fc17
@updates
glibc-devel.x86_642.15-57.fc17
@updates
glibc-headers.x86_64  2.15-57.fc17   @updates

gcc.x86_644.7.2-2.fc17
@updates
gcc-c++.x86_644.7.2-2.fc17
@updates
gcc-gfortran.x86_64   4.7.2-2.fc17
@updates
libgcc.i686   4.7.2-2.fc17
@updates
libgcc.x86_64 4.7.2-2.fc17   @updates


Thomas



On 19 November 2012 16:57, Szilárd Páll  wrote:

> Thomas & Albert,
>
> We are unable to reproduce the issue on FC 17 with glibc 2.15-58 and gcc
> 4.7.2.
>
> Please try to update your packages (you should have updates available for
> glibc), try recompiling with the latest 4.6 code and report back whether
> you succeed.
>
> Cheers,
>
> --
> Szilárd
>
>
> On Fri, Nov 16, 2012 at 4:31 PM, Szilárd Páll  >wrote:
>
> > Hi Albert,
> >
> > Apologies for hijacking your thread. Do you happen to have Fedora 17 as
> > well?
> >
> > --
> > Szilárd
> >
> >
> >
> > On Sun, Nov 4, 2012 at 10:55 AM, Albert  wrote:
> >
> >> hello:
> >>
> >>  I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2 x
> >> 1344 CUDA cores), and I got the following warnings:
> >>
> >> thank you very much.
> >>
> >> ---**messages--**
> >> -
> >>
> >> WARNING: On node 0: oversubscribing the available 0 logical CPU cores
> per
> >> node with 2 MPI processes.
> >>  This will cause considerable performance loss!
> >>
> >> 2 GPUs detected on host boreas:
> >>   #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> >> compatible
> >>   #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> >> compatible
> >>
> >> 2 GPUs auto-selected to be used for this run: #0, #1
> >>
> >> Using CUDA 8x8x8 non-bonded kernels
> >> Making 1D domain decomposition 1 x 2 x 1
> >>
> >> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
> >> We have just committed the new CPU detection code in this branch,
> >> and will commit new SSE/AVX kernels in a few days. However, this
> >> means that currently only the NxN kernels are accelerated!
> >> In the mean time, you might want to avoid production runs in 4.6.
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
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> >>
> >
> >
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-- 

==

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tev...@pharm.uoa.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [gmx-users] GPU warnings

[Szilárd Páll]

Thomas & Albert,

We are unable to reproduce the issue on FC 17 with glibc 2.15-58 and gcc
4.7.2.

Please try to update your packages (you should have updates available for
glibc), try recompiling with the latest 4.6 code and report back whether
you succeed.

Cheers,

--
Szilárd


On Fri, Nov 16, 2012 at 4:31 PM, Szilárd Páll wrote:

> Hi Albert,
>
> Apologies for hijacking your thread. Do you happen to have Fedora 17 as
> well?
>
> --
> Szilárd
>
>
>
> On Sun, Nov 4, 2012 at 10:55 AM, Albert  wrote:
>
>> hello:
>>
>>  I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2 x
>> 1344 CUDA cores), and I got the following warnings:
>>
>> thank you very much.
>>
>> ---**messages--**
>> -
>>
>> WARNING: On node 0: oversubscribing the available 0 logical CPU cores per
>> node with 2 MPI processes.
>>  This will cause considerable performance loss!
>>
>> 2 GPUs detected on host boreas:
>>   #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>> compatible
>>   #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>> compatible
>>
>> 2 GPUs auto-selected to be used for this run: #0, #1
>>
>> Using CUDA 8x8x8 non-bonded kernels
>> Making 1D domain decomposition 1 x 2 x 1
>>
>> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
>> We have just committed the new CPU detection code in this branch,
>> and will commit new SSE/AVX kernels in a few days. However, this
>> means that currently only the NxN kernels are accelerated!
>> In the mean time, you might want to avoid production runs in 4.6.
>>
>> --
>> 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/Searchbefore
>>  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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[gmx-users] which version it is?

[Albert]

hello:

 I found a charmm36.tar.gz in Gromacs website


 GROMACS 4.5.4 version of the CHARMM36 force field files. These updated 
CHARMM lipids allow the all-atom simulations of membrane and 
membrane-protein systems without the use of surface tension. Check out 
the forcefield.doc for more information regarding these files

71.65 kB15:42, 25 Sep 2012TomPiggot


I am just wondering, is the the one with 
CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids?


thank you very much
best
Albert
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[gmx-users] min + capped peptide

[Bahar Mehrpuyan]

Hi gmx users

I want to cap my peptide (adding ACE & NAC) with Avogadro package , my question 
is , should I minimize the capped peptide with forcefields(molecular mechanics) 
available in avogadro, then use it in the simulation? or just simulation 
procedures (minimization and equilibration) is sufficient for minimizing the 
peptide structure.

thanks in advance
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Re: [gmx-users] strange protonate state

[David van der Spoel]

On 2012-11-19 10:42, Albert wrote:

On 11/19/2012 10:27 AM, David van der Spoel wrote:

On 2012-11-19 09:57, Albert wrote:

hello:

   I've got a K+ near an Asp residue. I found that If I include the K+
in H++ calculation, the Asp is deprotonated while it is protonated if I
didn't include it. I am quite confused for this. I am just wondering
will the g_protonate will solve this problem?

thank you very much.
best
Albert

This makes sense! The environment is made for a neutral group, which
you get by either having a K+ or a proton near the Asp.

Normal pdb2gmx will give you the correct topology.



hello David:

  thanks a lot for such kind reply and comments.
  Is there any paper concerning on this ion issue? The pdb2gmx make
correct protonation state of residues in most case, however for some
special case we probably need more solid evidence to be confirmed. Since
the protonation state of residue have great impact on later MD productions.


No paper, just basic biochemistry.
In case you suspect an amino-acid should NOT have the default 
protonation you can run pdb2gmx interactively. This is however your 
responsibility as the algorithm is not perfect, in fact it only checks 
the protonation of histidine residues.




thank you very  much.
best
Albert



--
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] (no subject)

[behnoosh Bahadori]

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Re: [gmx-users] Save frames of trajectory file

[Erik Marklund]

trjconv

19 nov 2012 kl. 10.47 skrev Shima Arasteh:

> Dear gmx users,
> 
> Is there any command in GROMACS, which I can use it to save frames of 
> trajectory file in pdb format?
> 
> 
> 
> Sincerely,
> Shima 
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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[gmx-users] Save frames of trajectory file

[Shima Arasteh]

Dear gmx users,

Is there any command in GROMACS, which I can use it to save frames of 
trajectory file in pdb format?



Sincerely,
Shima 
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Re: [gmx-users] strange protonate state

[Albert]

On 11/19/2012 10:27 AM, David van der Spoel wrote:

On 2012-11-19 09:57, Albert wrote:

hello:

   I've got a K+ near an Asp residue. I found that If I include the K+
in H++ calculation, the Asp is deprotonated while it is protonated if I
didn't include it. I am quite confused for this. I am just wondering
will the g_protonate will solve this problem?

thank you very much.
best
Albert
This makes sense! The environment is made for a neutral group, which 
you get by either having a K+ or a proton near the Asp.


Normal pdb2gmx will give you the correct topology.



hello David:

 thanks a lot for such kind reply and comments.
 Is there any paper concerning on this ion issue? The pdb2gmx make 
correct protonation state of residues in most case, however for some 
special case we probably need more solid evidence to be confirmed. Since 
the protonation state of residue have great impact on later MD productions.


thank you very  much.
best
Albert
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Re: [gmx-users] strange protonate state

[David van der Spoel]

On 2012-11-19 09:57, Albert wrote:

hello:

   I've got a K+ near an Asp residue. I found that If I include the K+
in H++ calculation, the Asp is deprotonated while it is protonated if I
didn't include it. I am quite confused for this. I am just wondering
will the g_protonate will solve this problem?

thank you very much.
best
Albert
This makes sense! The environment is made for a neutral group, which you 
get by either having a K+ or a proton near the Asp.


Normal pdb2gmx will give you the correct topology.

--
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] strange protonate state

[Albert]

hello:

  I've got a K+ near an Asp residue. I found that If I include the K+ 
in H++ calculation, the Asp is deprotonated while it is protonated if I 
didn't include it. I am quite confused for this. I am just wondering 
will the g_protonate will solve this problem?


thank you very much.
best
Albert
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