[gmx-users] mdrun error

[Collins Nganou]

Dear Users,

when trying to run the following command:
mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb
I have received the error below.



Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision)
Starting 2 threads

---
Program mdrun, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 6005

Fatal error:
Domain decomposition does not support simple neighbor searching, use grid
searching or use particle decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I am looking any suggestion that can help me to overcome this error.

Best regards

Albert Collins
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Re: [gmx-users] velocity-verlet giving nans

[Elton Carvalho]

On Fri, Jun 7, 2013 at 11:52 AM, Mark Abraham  wrote:

> If you want to suggest fixing any possible problem, please file an issue at
> redmine.gromacs.org
>

There is already a report in redmine with a suggestion on how to deal
with NaNs: http://redmine.gromacs.org/issues/941

On Thu, Jun 6, 2013 at 4:38 AM, Sikandar Mashayak wrote:
>  when I run 'mdrun' I am getting 'nan' in output from the
> first step itself.

Does mdrun keep running with NaN after NaN or does it stop with an
error message (or segfault for that matter)?

Cheers,
--
Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
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Re: [gmx-users] Comparing the simulation

[Justin Lemkul]

On 7/20/13 9:12 AM, rama david wrote:

Dear Justin,
Thank you for your Prompt Reply.

I run a at least 4-5 run of each peptide.
The result are like the xx peptide form beta structure early than yy
peptide in each run.
I just used the different tau_P ( relaxation time ) for NPT and MD
production run.
XX tau_p = 2   YY tau_p= 1


NVT parameter are same.

On these basis can I make the interpretation that XX form beta sheet
structure early than YY
though they uses the same barostat but different tau_P ??



I've already expressed by opinion on that in the previous post.

-Justin



With Best Wishes and Regards,
Rama David




On Sat, Jul 20, 2013 at 4:49 PM, Justin Lemkul  wrote:




On 7/20/13 5:27 AM, rama david wrote:


Dear Friends,
   I did the Simulation study for self
assembly of peptides . ( I used G96 53a6 FF )

In First Experiment, I put the two XX peptide far from each other 2.0 nm,
   and run the simulation.
In the second experiment I put the two YY peptide seperated by 2.0 nm.
and run the simulation.
In nvt I used the sane parameter, but In NPT, MD simulation I run
the Parrinello-Rahman barostat with tau_P 2.0 ns for XX peptide and tau_P
1
for
YY peptide.
I found that peptide YY interaction start at 80ns and XX interaction
start at 10 ns.


 I have following Question.
   1>.Is it possible to compare  two MD simulation which used the
same barostat   but having the different tau_P ( Relaxation time).



You'll have to examine pressure distributions very carefully, but I am
inherently suspicious of trying to salvage results that were based on a
mistake.


  2>. Could I make the interpretation that  XX peptide start

interact
more early   than YY ??



Based on one simulation of each?  No.


  3>>. Would we compare  the result between the simulation that uses the

different barostat ant thermostat but still using the same Force field.



If you are altering both thermostat and barostat, I would be extremely
skeptical of the results.  Apply consistent methods.

-Justin

--
==**

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul@outerbanks.umaryland.**edu  |
(410) 706-7441

==**
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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] atomtypes in .n2t

[Justin Lemkul]

On 7/20/13 7:35 AM, afsaneh maleki wrote:

Dear users


To generate a topology file for an arbitrary molecule, I used g_x2top
program.

  I added following lines to atomname2type.n2t:

..

..

C  opls_145B   0.080627   12.0110   3 C 0.1395 C 0.1395  C 0.149

C  opls_145B   0.091698   12.0110   3 C 0.149  C 0.1395  C 0.1395



You're going to have problems.  Both of these lines specify the same criteria to 
assign different charges to a given atom.



..

But, generated topology file is as the following:

.

[ atoms ]

;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
  chargeB  massB

..

..

 17   opls_145  1TPTC15  1   0.037549 12.011   ;
qtot -0.4087

 18   opls_145  1TPTC12  1   0.037549 12.011   ;
qtot -0.3712

..

I don’t know, why g_x2top program replaces opls_145B (in .n2t) with
opls_145 atom type to generate topology file?



Apparently the opls_145B criteria (distances to neighboring atoms) are not 
satisfied, but the opls_145 criteria are.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Re: Question on Hessian and forces not being preserved on restart with Hessian calculation?

[Michael Shirts]

Problem partly addressed.  If I run normal modes in -nt 1, then I get
the same force as after the minimization.

I'll file a redmine.

On Sat, Jul 20, 2013 at 9:43 AM, Michael Shirts  wrote:
> To follow up -- if I try to minimize again using -t, I get the same
> low forces as in the minimization in the previous step.  So it appears
> to be something with what do_nm is doing, not with errors in the
> output structure.
>
> On Sat, Jul 20, 2013 at 9:37 AM, Michael Shirts  wrote:
>> When I minimize a structure, I can get down to the force max being <0.01
>>
>> Low-Memory BFGS Minimizer converged to Fmax < 0.01 in 6839 steps
>> Potential Energy  = -5.12340607768673e+03
>> Maximum force =  6.68907856457542e-03 on atom 3029
>> Norm of force =  2.19978176343026e-03
>>
>> kJ/nm.  However, when I try to perform a normal mode analysis, it
>> complains that the maximum energy is >30 kJ/mn.
>>
>>
>> Non-cutoff electrostatics used, forcing full Hessian format.
>> Allocating Hessian memory...
>>
>> Maximum force: 3.91984e+01
>> Maximum force probably not small enough to ensure that you are in an
>> energy well. Be aware that negative eigenvalues may occur when the
>> resulting matrix is diagonalized.
>>
>> I've restarted from the binary .trr output (-t option) , and I'm using
>> double precision. Any suggestions as to why the force max is not the
>> asme on restarting?  Only difference is going from l-bfgs to nm.
>>
>> I've seen some older comments on this, but no resolution and nothing recent.
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[gmx-users] Re: Question on Hessian and forces not being preserved on restart with Hessian calculation?

[Michael Shirts]

To follow up -- if I try to minimize again using -t, I get the same
low forces as in the minimization in the previous step.  So it appears
to be something with what do_nm is doing, not with errors in the
output structure.

On Sat, Jul 20, 2013 at 9:37 AM, Michael Shirts  wrote:
> When I minimize a structure, I can get down to the force max being <0.01
>
> Low-Memory BFGS Minimizer converged to Fmax < 0.01 in 6839 steps
> Potential Energy  = -5.12340607768673e+03
> Maximum force =  6.68907856457542e-03 on atom 3029
> Norm of force =  2.19978176343026e-03
>
> kJ/nm.  However, when I try to perform a normal mode analysis, it
> complains that the maximum energy is >30 kJ/mn.
>
>
> Non-cutoff electrostatics used, forcing full Hessian format.
> Allocating Hessian memory...
>
> Maximum force: 3.91984e+01
> Maximum force probably not small enough to ensure that you are in an
> energy well. Be aware that negative eigenvalues may occur when the
> resulting matrix is diagonalized.
>
> I've restarted from the binary .trr output (-t option) , and I'm using
> double precision. Any suggestions as to why the force max is not the
> asme on restarting?  Only difference is going from l-bfgs to nm.
>
> I've seen some older comments on this, but no resolution and nothing recent.
-- 
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[gmx-users] Question on Hessian and forces not being preserved on restart with Hessian calculation?

[Michael Shirts]

When I minimize a structure, I can get down to the force max being <0.01

Low-Memory BFGS Minimizer converged to Fmax < 0.01 in 6839 steps
Potential Energy  = -5.12340607768673e+03
Maximum force =  6.68907856457542e-03 on atom 3029
Norm of force =  2.19978176343026e-03

kJ/nm.  However, when I try to perform a normal mode analysis, it
complains that the maximum energy is >30 kJ/mn.


Non-cutoff electrostatics used, forcing full Hessian format.
Allocating Hessian memory...

Maximum force: 3.91984e+01
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.

I've restarted from the binary .trr output (-t option) , and I'm using
double precision. Any suggestions as to why the force max is not the
asme on restarting?  Only difference is going from l-bfgs to nm.

I've seen some older comments on this, but no resolution and nothing recent.
-- 
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Re: [gmx-users] Comparing the simulation

[rama david]

Dear Justin,
Thank you for your Prompt Reply.

   I run a at least 4-5 run of each peptide.
The result are like the xx peptide form beta structure early than yy
peptide in each run.
I just used the different tau_P ( relaxation time ) for NPT and MD
production run.
XX tau_p = 2   YY tau_p= 1


NVT parameter are same.

On these basis can I make the interpretation that XX form beta sheet
structure early than YY
though they uses the same barostat but different tau_P ??


With Best Wishes and Regards,
Rama David




On Sat, Jul 20, 2013 at 4:49 PM, Justin Lemkul  wrote:

>
>
> On 7/20/13 5:27 AM, rama david wrote:
>
>> Dear Friends,
>>   I did the Simulation study for self
>> assembly of peptides . ( I used G96 53a6 FF )
>>
>> In First Experiment, I put the two XX peptide far from each other 2.0 nm,
>>   and run the simulation.
>> In the second experiment I put the two YY peptide seperated by 2.0 nm.
>> and run the simulation.
>>In nvt I used the sane parameter, but In NPT, MD simulation I run
>> the Parrinello-Rahman barostat with tau_P 2.0 ns for XX peptide and tau_P
>> 1
>> for
>> YY peptide.
>>I found that peptide YY interaction start at 80ns and XX interaction
>> start at 10 ns.
>>
>>
>> I have following Question.
>>   1>.Is it possible to compare  two MD simulation which used the
>> same barostat   but having the different tau_P ( Relaxation time).
>>
>>
> You'll have to examine pressure distributions very carefully, but I am
> inherently suspicious of trying to salvage results that were based on a
> mistake.
>
>
>  2>. Could I make the interpretation that  XX peptide start
>> interact
>> more early   than YY ??
>>
>>
> Based on one simulation of each?  No.
>
>
>  3>>. Would we compare  the result between the simulation that uses the
>> different barostat ant thermostat but still using the same Force field.
>>
>>
> If you are altering both thermostat and barostat, I would be extremely
> skeptical of the results.  Apply consistent methods.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
> --
> 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!
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>
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[gmx-users] Setting attractive part (C6 parameter) zero in non-bonded parameters

[Suman Chakrabarty]

Hello,

Following the Section 5.3.2 of the manual, I have tried to set the C6
term of the non-bonded (Lennard-Jones) interaction to zero as follows:

"When sigma and epsilon need to be supplied (rules 2 and 3), it
would seem it is impossible to have a non-zero C12 combined with a
zero C6 parameter. However, providing a negative sigma will do
exactly that, such that C6 is set to zero and C12 is calculated
normally. This situation represents a special case in reading the
value of sigma, and nothing more."

Unfortunately when I try this the potential energy of the system becomes "nan":
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
LJ (SR)   Coulomb (SR)   Coul. recip.  PotentialKinetic En.
nan   -1.76446e+05   -1.26632e+03nan2.30786e+04
   Total Energy  Conserved En.Temperature Pressure (bar)
nannan2.25008e+02nan

With the positive sign for sigma in the topology file, the same
structure gives the following energetics:
   Energies (kJ/mol)
LJ (SR)   Coulomb (SR)   Coul. recip.  PotentialKinetic En.
4.56607e+04   -1.76446e+05   -1.26632e+03   -1.32051e+052.30777e+04
   Total Energy  Conserved En.Temperature Pressure (bar)
   -1.08974e+05   -1.08974e+052.24999e+023.52545e+04

=
Here I am trying to look at a single solute atom (I change the sign of
the sigma value for this atom only) in a box of TIP4P water.
Strangely, I encounter this "nan" problem only for comb-rule=3.
Whereas, for comb-rule=2, energetics are reasonable, but it appears
that sigma_ij between the solute and solvent becomes very small (as
evident for rdf of water oxygen atoms around this solute atom). This
would imply that the negative value of sigma_i for the solute is being
retained as it is, so in 0.5*(sigma_i + sigma_j) they cancel each
other to large extent.

It seems there is a bug in the treatment of the negative sigma values
as described in the manual. Please let me know if you think I am
making a mistake somewhere. Thanks.

Best regards,
Suman.
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[gmx-users] Compilation problem with Gromacs 4.5.7 (autoconf only)

[Suman Chakrabarty]

Hello,

I am not sure whether this is a known problem, but it seems
gromacs-4.5.7 compilation using autoconf tool is still broken (at
least for me). The ./configure step completes without any error. But
"make" fails with the following error regarding not finding certain
version of aclocal and automake (I have aclocal-1.11 and automake-1.11
installed. Is there any new strict version requirement in 4.5.7?). By
the way, compilation of 4.5.6 completes successfully using autoconf
tool, and 4.5.7 works with cmake compilation.

The error at the "make" step:

cd . && /bin/bash /home/suman/sources/gromacs-4.5.7/config/missing
--run aclocal-1.10 -I config
/home/suman/sources/gromacs-4.5.7/config/missing: line 52:
aclocal-1.10: command not found
WARNING: `aclocal-1.10' is missing on your system.  You should only need it if
 you modified `acinclude.m4' or `configure.ac'.  You might want
 to install the `Automake' and `Perl' packages.  Grab them from
 any GNU archive site.
 cd . && /bin/bash /home/suman/sources/gromacs-4.5.7/config/missing
--run automake-1.10 --foreign
/home/suman/sources/gromacs-4.5.7/config/missing: line 52:
automake-1.10: command not found
WARNING: `automake-1.10' is missing on your system.  You should only need it if
 you modified `Makefile.am', `acinclude.m4' or `configure.ac'.
 You might want to install the `Automake' and `Perl' packages.
 Grab them from any GNU archive site.
cd . && /bin/bash /home/suman/sources/gromacs-4.5.7/config/missing
--run autoconf
configure.ac:509: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call
detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
configure.ac:509: the top level
configure.ac:525: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call
detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
configure.ac:525: the top level
configure.ac:17: error: possibly undefined macro: AM_INIT_AUTOMAKE
  If this token and others are legitimate, please use m4_pattern_allow.
  See the Autoconf documentation.
configure.ac:20: error: possibly undefined macro: AM_CONFIG_HEADER
configure.ac:26: error: possibly undefined macro: AC_ENABLE_SHARED
configure.ac:27: error: possibly undefined macro: AC_DISABLE_SHARED
configure.ac:49: error: possibly undefined macro: AM_CONDITIONAL
configure.ac:372: error: possibly undefined macro: AM_PROG_AS
configure.ac:609: error: possibly undefined macro: AC_LIBTOOL_WIN32_DLL
configure.ac:610: error: possibly undefined macro: AC_LIBTOOL_DLOPEN
configure.ac:611: error: possibly undefined macro: AC_PROG_LIBTOOL
configure.ac:826: error: possibly undefined macro: AM_WITH_DMALLOC
make: *** [configure] Error 1

Best regards,
Suman.
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[gmx-users] old and new versions of gromacs

[mohammad agha]

Dear Justin,

Thank you very much from your response.

Best Regards
Sara





 From: Justin Lemkul 
To: mohammad agha ; Discussion list for GROMACS users 
 
Sent: Saturday, July 20, 2013 3:47 PM
Subject: Re: [gmx-users] old and new versions of gromacs
 



On 7/20/13 2:58 AM, mohammad agha wrote:
> Dear Gromacs Specialists
>
> I already worked with Gromacs-4.5.4. In the Gromacs site has been released 
> new several versions. Has the old version (4.5.4) defects? Or are the new 
> versions more complete? I want to continiue my simulations with 4.5.4, are 
> there problems for it?
> I compared the manual of 4.5.4 and 4.6.3. In the 4.5.4 there are 88 commands 
> and in 4.6.3 there are 96 commands.
>

Every new version has release notes associated with it so you know what has 
changed.

http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x

> If I want to install the 4.6.3 in ubuntu 12.10, what is the way of 
> installation?
>

http://www.gromacs.org/Documentation/Installation_Instructions

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] atomtypes in .n2t

[afsaneh maleki]

Dear users


To generate a topology file for an arbitrary molecule, I used g_x2top
program.

 I added following lines to atomname2type.n2t:

..

..

C  opls_145B   0.080627   12.0110   3 C 0.1395 C 0.1395  C 0.149

C  opls_145B   0.091698   12.0110   3 C 0.149  C 0.1395  C 0.1395

..

But, generated topology file is as the following:

.

[ atoms ]

;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
 chargeB  massB

..

..

17   opls_145  1TPTC15  1   0.037549 12.011   ;
qtot -0.4087

18   opls_145  1TPTC12  1   0.037549 12.011   ;
qtot -0.3712

..

I don’t know, why g_x2top program replaces opls_145B (in .n2t) with
opls_145 atom type to generate topology file?

Thanks in advance,

Afsaneh
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Re: [gmx-users] Comparing the simulation

[Justin Lemkul]

On 7/20/13 5:27 AM, rama david wrote:

Dear Friends,
  I did the Simulation study for self
assembly of peptides . ( I used G96 53a6 FF )

In First Experiment, I put the two XX peptide far from each other 2.0 nm,
  and run the simulation.
In the second experiment I put the two YY peptide seperated by 2.0 nm.
and run the simulation.
   In nvt I used the sane parameter, but In NPT, MD simulation I run
the Parrinello-Rahman barostat with tau_P 2.0 ns for XX peptide and tau_P 1
for
YY peptide.
   I found that peptide YY interaction start at 80ns and XX interaction
start at 10 ns.


I have following Question.
  1>.Is it possible to compare  two MD simulation which used the
same barostat   but having the different tau_P ( Relaxation time).



You'll have to examine pressure distributions very carefully, but I am 
inherently suspicious of trying to salvage results that were based on a mistake.



2>. Could I make the interpretation that  XX peptide start interact
more early   than YY ??



Based on one simulation of each?  No.


3>>. Would we compare  the result between the simulation that uses the
different barostat ant thermostat but still using the same Force field.



If you are altering both thermostat and barostat, I would be extremely skeptical 
of the results.  Apply consistent methods.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] old and new versions of gromacs

[Justin Lemkul]

On 7/20/13 2:58 AM, mohammad agha wrote:

Dear Gromacs Specialists

I already worked with Gromacs-4.5.4. In the Gromacs site has been released new 
several versions. Has the old version (4.5.4) defects? Or are the new versions 
more complete? I want to continiue my simulations with 4.5.4, are there 
problems for it?
I compared the manual of 4.5.4 and 4.6.3. In the 4.5.4 there are 88 commands 
and in 4.6.3 there are 96 commands.



Every new version has release notes associated with it so you know what has 
changed.

http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x


If I want to install the 4.6.3 in ubuntu 12.10, what is the way of installation?



http://www.gromacs.org/Documentation/Installation_Instructions

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Comparing the simulation

[rama david]

Dear Friends,
 I did the Simulation study for self
assembly of peptides . ( I used G96 53a6 FF )

In First Experiment, I put the two XX peptide far from each other 2.0 nm,
 and run the simulation.
In the second experiment I put the two YY peptide seperated by 2.0 nm.
and run the simulation.
  In nvt I used the sane parameter, but In NPT, MD simulation I run
the Parrinello-Rahman barostat with tau_P 2.0 ns for XX peptide and tau_P 1
for
YY peptide.
  I found that peptide YY interaction start at 80ns and XX interaction
start at 10 ns.


   I have following Question.
 1>.Is it possible to compare  two MD simulation which used the
same barostat   but having the different tau_P ( Relaxation time).

2>. Could I make the interpretation that  XX peptide start interact
more early   than YY ??

3>>. Would we compare  the result between the simulation that uses the
different barostat ant thermostat but still using the same Force field.


I am looking forward for reply.


With Best Wishes,
Rama David
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Re: [gmx-users] GROMACS 4.6.3 Static Linking

[Dr. Vitaly Chaban]

Soneone said here that static versions are impossible for Cray...



Dr. Vitaly V. Chaban


On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner wrote:

> Hi
>
> I am having problems creating static versions of the GROMACS binaries for
> a Cray XE6 (www.hector.ac.uk). The build process I am using is documented
> at:
>
> http://www.hector.ac.uk/**support/documentation/**
> software/gromacs/compiling_4-**6-1_phase3.php
>
> and successfully produced static binaries for 4.6.1. Has something changed
> in the new version?
>
> In particular, I am setting:
>
> -DCMAKE_SKIP_RPATH=YES
> -DBUILD_SHARED_LIBS=OFF
> -DGMX_PREFER_STATIC_LIBS=ON
> -DCMAKE_C_FLAGS="-static -O3 -ftree-vectorize -ffast-math -funroll-loops"
> -DCMAKE_CXX_FLAGS="-static -O3 -ftree-vectorize -ffast-math -funroll-loops"
>
> but still get dynamic executables:
>
> gmx@hector-xe6-5:~/4.6.3-**phase3/bin> ldd grompp
> linux-vdso.so.1 =>  (0x7fff00da2000)
> libm.so.6 => /lib64/libm.so.6 (0x7f50dc58f000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x7f50dc371000)
> libAtpSigHandler.so.0 => /opt/cray/lib64/**libAtpSigHandler.so.0
> (0x7f50dc16b000)
> libgfortran.so.3 => /opt/gcc/4.7.2/snos/lib64/**libgfortran.so.3
> (0x7f50dbe54000)
> libscicpp_gnu.so.2 => /opt/cray/lib64/libscicpp_gnu.**so.2
> (0x7f50dbc4a000)
> libsci_gnu_mp.so.2 => /opt/cray/lib64/libsci_gnu_mp.**so.2
> (0x7f50d72ec000)
> libstdc++.so.6 => /opt/gcc/4.7.2/snos/lib64/**libstdc++.so.6
> (0x7f50d6fdf000)
> libfftw3_mpi.so.3 => /opt/cray/lib64/libfftw3_mpi.**so.3
> (0x7f50d6dc6000)
> libfftw3f_mpi.so.3 => /opt/cray/lib64/libfftw3f_mpi.**so.3
> (0x7f50d6bae000)
> libfftw3_threads.so.3 => /opt/cray/lib64/libfftw3_**threads.so.3
> (0x7f50d69a6000)
> libfftw3f_threads.so.3 => /opt/cray/lib64/libfftw3f_**threads.so.3
> (0x7f50d679d000)
> libfftw3.so.3 => /opt/cray/lib64/libfftw3.so.3 (0x7f50d63a2000)
> libfftw3f.so.3 => /opt/cray/lib64/libfftw3f.so.3
> (0x7f50d5f7c000)
> libmpich_gnu_47.so.1 => /opt/cray/lib64/libmpich_gnu_**47.so.1
> (0x7f50d5add000)
> libmpichf90_gnu_47.so.1 => /opt/cray/lib64/libmpichf90_**gnu_47.so.1
> (0x7f50d58da000)
> libmpl.so.0 => /opt/cray/lib64/libmpl.so.0 (0x7f50d56d5000)
> librt.so.1 => /lib64/librt.so.1 (0x7f50d54cb000)
> libxpmem.so.0 => /opt/cray/xpmem/default/lib64/**libxpmem.so.0
> (0x7f50d52c9000)
> libdmapp.so.1 => /opt/cray/dmapp/default/lib64/**libdmapp.so.1
> (0x7f50d5092000)
> libugni.so.0 => /opt/cray/ugni/default/lib64/**libugni.so.0
> (0x7f50d4e72000)
> libpmi.so.0 => /opt/cray/pmi/default/lib64/**libpmi.so.0
> (0x7f50d4c51000)
> libalpslli.so.0 => /usr/lib/alps/libalpslli.so.0
> (0x7f50d4a4e000)
> libalpsutil.so.0 => /usr/lib/alps/libalpsutil.so.0
> (0x7f50d4849000)
> libudreg.so.0 => /opt/cray/udreg/default/lib64/**libudreg.so.0
> (0x7f50d4641000)
> libgomp.so.1 => /opt/gcc/4.7.2/snos/lib64/**libgomp.so.1
> (0x7f50d4432000)
> libc.so.6 => /lib64/libc.so.6 (0x7f50d40d3000)
> libgcc_s.so.1 => /opt/gcc/4.7.2/snos/lib64/**libgcc_s.so.1
> (0x7f50d3ebd000)
> /lib/ld64.so.1 => /lib64/ld-linux-x86-64.so.2 (0x7f50dc812000)
> libquadmath.so.0 => /opt/gcc/4.7.2/snos/lib64/**libquadmath.so.0
> (0x7f50d3c87000)
> libcray_memcpy.so.0 => /opt/cray/lib64/libcray_**memcpy.so.0
> (0x7f50d3a84000)
> libopa.so.1 => /opt/cray/lib64/libopa.so.1 (0x7f50d3882000)
> librca.so.0 => /opt/cray/rca/default/lib64/**librca.so.0
> (0x7f50d367d000)
> libdl.so.2 => /lib64/libdl.so.2 (0x7f50d3479000)
>
> Any ideas?
> Andy
>
>
> ==**===
> Dr Andrew R. Turner
>  e: a.tur...@epcc.ed.ac.uk
>  skype: aturner-epcc
>  t: +44 (0)131 651 3578
>  p: EPCC, University of Edinburgh EH9 3JZ
> ==**===
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
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[gmx-users] old and new versions of gromacs

[mohammad agha]

Dear Gromacs Specialists

I already worked with Gromacs-4.5.4. In the Gromacs site has been released new 
several versions. Has the old version (4.5.4) defects? Or are the new versions 
more complete? I want to continiue my simulations with 4.5.4, are there 
problems for it?
I compared the manual of 4.5.4 and 4.6.3. In the 4.5.4 there are 88 commands 
and in 4.6.3 there are 96 commands. 

If I want to install the 4.6.3 in ubuntu 12.10, what is the way of installation?

Please help me.
Thanks in advance.
Best Regards
Sara
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[gmx-users] old and new versions of gromacs

[mohammad agha]

Dear Gromacs Specialists

I already worked with Gromacs-4.5.4. In the Gromacs site has been released new 
several versions. Has the old version (4.5.4) defects? Or are the new versions 
more complete? I want to continiue my simulations with 4.5.4, are there 
problems for it?
I compared the manual of 4.5.4 and 4.6.3. In the 4.5.4 there are 88 commands 
and in 4.6.3 there are 96 commands. 

If I want to install the 4.6.3 in ubuntu 12.10, what is the way of installation?

Please help me.
Thanks in advance.
Best Regards
Sara
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