Re: [gmx-users] how small rcoulomb can be

[Florian Dommert]

Hello,

 tuning the pme to an optimal balance between accuracy and speed is indeed a 
nontrivial task. As already mentioned a too small cutoff in real space will 
require a large cutoff in reciprocal space and therefore the parallel scaling 
will be the problem. If you post all files necessary to generate a tpr, then I 
can tell you some settings for a desired accuracy.

Unfortunately the routine is not ready to push it to the master branch. There 
are some things to clarify. However to be able to use it you have to patch the 
file ewald_util.c a little bit, that it accepts negative values that you can 
input the parameter beta directly. But this is trivial. Just put

if (dtol<0.0)
return -dtol;

at the beginning of the routine and everything is fine. Then you can input just 
the negative value of the desired beta value at the ewald_rtol section of the 
mdp file and
everything is fine. 

/Flo


On 18.06.2010, at 18:40, Gaurav Goel wrote:

> I will re-ask my question as it didn't come out right in previous
> mail. Read below.
> 
> On Wed, Jun 16, 2010 at 6:11 PM, Mark Abraham  wrote:
>> 
>> 
>> - Original Message -
>> From: Gaurav Goel 
>> Date: Thursday, June 17, 2010 5:21
>> Subject: [gmx-users] how small rcoulomb can be
>> To: Discussion list for GROMACS users 
>> 
>>> For my NPT/NVT simulations I'm using a BKS potential for dispersion
>>> interactions (VdWtype=USER)  which has a cut-off of 0.55
>>> nm. I also
>>> set rcoulomb=rlist=0.55 nm.
>>> 
>>> My first question is regarding the choice of rcoulomb=0.55nm. Any
>>> thoughts on whether this rcoulomb is large enough to ascertain that
>>> real space electrostatics interactions are fairly small (in comparison
>>> to total coulombic interactions)?
>> 
>> That's around half the size of typical rcoulomb values used for PME, so
>> you'll need to adjust ewald_rtol and fourier_spacing to a considerable
>> degree in order that the electrostatics your PME model is comparably
>> accurate. If this model has been used with PME in the past, then you will
>> have some guidance in its literature (though GROMACS does not make it easy
>> to choose beta directly). This will mean the reciprocal-space processors are
>> doing lots more work than normal, and you'll want to set -npme to be half of
>> -np, or maybe zero. Even so, your parallel scaling will be noticeably worse
>> than normal PME.
> 
> Thanks for your reply Mark. Any thoughts on instead increasing
> rcoulomb and rlist. Will that be more efficient and/or accurate rather
> than trying to adjust ewald_rtol and fourier_spacing with a very short
> rcoulomb? In literature I found that the optimal value people have
> used for beta is, beta*L=10.
> 
> In my simulations, for rcoulomb=0.55, beta*L=15.52
>rcoulomb=0.9, beta*L=   9.49
> How can I obtain the magnitude of maximum wave vector (i.e., 'm' in
> Eq. 4.159 of manual 4.0)?
> 
> I have a separate question in regards to (conserved) energy drift in a
> NVT simulation.
> 
> I first equilibrated my system for 1 ns in NPT ensemble. Then, I
> turned-off the pressure coupling, further equilibrated my system for 1
> ns In NVT ensemble [N=2160, V=20.43 nm^3, T=4000K; rcoulomb=rlist=0.9,
> rvdw=0.55, nstlist=5]. Then in a production run of 3.5ns I get
> following energy drifts:
> Statistics over 3549897 steps [ 1000. thru 4549.8960 ps ], 1 data sets
> All averages are exact over 3549897 steps
> 
> Energy  Average   RMSD Fluct.  Drift  
> Tot-Drift
> ---
> Conserved En.-3.65264e+06  1893673.102718.4782
>  65595.7
> 
> i.e. drift=0.16 kT/ns.
> 
> If nstlist=10, drift= 0.5kT/ns
> 
> Should I worry about these drifts?
> 
> -Gaurav
>> 
>> Mark
>> 
>>> My second question is in regards to doing long (~15-100 ns) NVE
>>> simulations. It appears using coulombtype=PME-Switch will be the best
>>> option to accurately conserve energy. Any thoughts on how to choose
>>> rcoulomb_switch and rcoulomb?
>>> 
>>> Thanks,
>>> Gaurav
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[gmx-users] No default Proper Dih. types

[fancy2012]

Dear GMX users,
 
When I run grompp, I got this error " No default Proper Dih. types", how should 
I figure it out? Thanks in advance!
 
All the best,
fancy-- 
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[gmx-users] selection of group in do_dssp

[shahab shariati]

Dear gromacs users

When I used do_dssp for my protein analysis, gromacs asked me [select a
group]. what is the best group for this command?

any help will highly appreciated.
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Re: [gmx-users] selection of group in do_dssp

[Justin A. Lemkul]

shahab shariati wrote:

Dear gromacs users
 
When I used do_dssp for my protein analysis, gromacs asked me [select a 
group]. what is the best group for this command?


http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp

-Justin

 
any help will highly appreciated.




--


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 default Proper Dih. types

[Justin A. Lemkul]

fancy2012 wrote:

Dear GMX users,
 
When I run grompp, I got this error " No default Proper Dih. types", how 
should I figure it out? Thanks in advance!
 


Whatever force field you're trying to use does not have a dihedral term for that 
type of dihedral.  Either obtain suitable parameters from the literature, 
parameterize it yourself, or use a different force field that can accommodate 
this term.


-Justin


All the best,
fancy



--


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 default Proper Dih. types

[#ZHAO LINA#]

Check your error message more,
They will tell you which line in which .itp file there is No default Proper 
Dih. types.

lina


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Saturday, June 19, 2010 8:54 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] No default Proper Dih. types

fancy2012 wrote:
> Dear GMX users,
>
> When I run grompp, I got this error " No default Proper Dih. types", how
> should I figure it out? Thanks in advance!
>

Whatever force field you're trying to use does not have a dihedral term for that
type of dihedral.  Either obtain suitable parameters from the literature,
parameterize it yourself, or use a different force field that can accommodate
this term.

-Justin

> All the best,
> fancy
>

--


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] Merge Trajectories

[John Shultz]

Hi GMX Users,

I am trying to merge some trajectories. Some of the trajectories are
not matching correctly. There is a discrepancy in the number of atoms.
Is there a way to report on the atom count for all these trajectories
so I can know which ones to exclude?

trjcat -f */*.xtc


---
Program trjcat, VERSION 4.0.5
Source code file: gmx_trjcat.c, line: 100

Fatal error:

Different numbers of atoms (3884/3907) in files
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Re: [gmx-users] Merge Trajectories

[Justin A. Lemkul]

John Shultz wrote:

Hi GMX Users,

I am trying to merge some trajectories. Some of the trajectories are
not matching correctly. There is a discrepancy in the number of atoms.
Is there a way to report on the atom count for all these trajectories
so I can know which ones to exclude?



Use gmxcheck.

-Justin


trjcat -f */*.xtc


---
Program trjcat, VERSION 4.0.5
Source code file: gmx_trjcat.c, line: 100

Fatal error:

Different numbers of atoms (3884/3907) in files


--


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] How to increase the tolerance for conjugate gradient minimization

[Erik Lindahl]

Hi Arthur,

Two answers:

It's a pretty fundamental result on numerical analysis that you can only 
achieve a tolerance that is sqrt(EPS), where EPS is your floating-point 
accuracy. If you need better tolerance you might have to try double precision.

Be careful to use e.g. switched interactions and a cutoff buffer, and you might 
want to emply L-BFGS minimization in the endgame.

However: this assumes you really need extremely low tolerance - the only normal 
application where that is the case is normal modes.

Cheers,

Erik



On Jun 4, 2010, at 7:54 PM, Arthur Roberts wrote:

> Hi, all,
> 
> Is there a way to increase the tolerance for Conjugate Gradient energy 
> minimization?
> 
> It seems that I can only get a Tolerance (Fmax) = 1e-4
> 
> emtol doesn't seem to do the trick.  I tried several values.
> 
> Much appreciated,
> Art
> 
> Dr. Arthur Roberts, Ph.D.
> University of California, San Diego
> Skaggs School of Pharmacy and Pharmaceutical Sciences
> 9500 Gilman Drive #0703
> La Jolla, CA 92093-0703
> 
> email: aroberts99...@yahoo.com
> cell: 206-850-7468
> skype=aroberts92122
> 
> 
> 
> -- 
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> 

--
Erik Lindahl 
Professor, Computational Structural Biology
Center for Biomembrane Research & Swedish e-Science Research Center
Department of Biochemistry & Biophysics, Stockholm University
Tel: +468164675 Cell: +46703844534

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[gmx-users] Openings for talented programmers/postdocs who'd like to work on simulations

[Erik Lindahl]

Hi,

We try not to do too many announcements on this list, but since there are a 
fair number of finishing PhDs/postdocs subscribing and we've found great talent 
before I figured it would be stupid not to mention it at least !


I'm looking for 2 talented postdocs/staff/programmers to join our growing team 
in Stockholm, starting this fall or later.

There are three main projects where we're looking for more manpower, and it 
will be possible to be involved in both as well as your own and the group's 
research on membrane proteins:

1. Stream computing. As you might have seen, Gromacs-4.5 will support GPUs, but 
this will grow much more with multi-node parallelization in the near future.

2. We are just embarking on a 3-year project to enable "exascaling" molecular 
simulation by trying to use tens of thousands (or more) processors for parallel 
adaptive simulation, in order to have life science applications make use of the 
largest machines in the world. 

3. Finally, we have an opening for an "application expert" in molecular 
simulations in collaboration with our local supercomputing center. To 50% this 
position will consist of long-term project support for Gromacs, while the other 
50% is spend on concrete research projects in our group. There is a reasonably 
large chance this could turn into a _permanent_ staff position.


Interested? Drop me a line and tell us a bit about yourself, what you're 
interested in (postdoc/programmer/staff), and what your plans look like 
time-wise! I'll be happy to tell you more about the work.



Cheers,

Erik

--
Erik Lindahl 
Professor, Computational Structural Biology
Center for Biomembrane Research & Swedish e-Science Research Center
Department of Biochemistry & Biophysics, Stockholm University
Tel: +468164675 Cell: +46703844534

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[gmx-users] Installing gromacs from git

[Sai Pooja]

Hi,

I followed the following steps to install gromacs from the git repository:

1) installed git
2) got a clone of gromacs using the anonymous option

3) installed fftw libraries using
./configure --enable-float --prefix=/fs/home/sm868
make
make install

4)export CPPFLAGS=-I/fs/home/sm868/include
   export LDFLAGS=-L/fs/home/sm868/include

6)ran ./bootstrap
7)ran ./configure --prefix=/fs/home/sm868
8)I get the error -
checking for sqrt in -lm... yes
checking for fftw3.h... yes
checking for main in -lfftw3f... no
configure: error: Cannot find fftw3f library

Can someone help me with this?


Pooja

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Re: [gmx-users] Installing gromacs from git

[Justin A. Lemkul]

Sai Pooja wrote:

Hi,

I followed the following steps to install gromacs from the git repository:

1) installed git
2) got a clone of gromacs using the anonymous option

3) installed fftw libraries using
./configure --enable-float --prefix=/fs/home/sm868
make
make install

4)export CPPFLAGS=-I/fs/home/sm868/include
   export LDFLAGS=-L/fs/home/sm868/include

6)ran ./bootstrap
7)ran ./configure --prefix=/fs/home/sm868
8)I get the error - 
checking for sqrt in -lm... yes

checking for fftw3.h... yes
checking for main in -lfftw3f... no
configure: error: Cannot find fftw3f library



You set your LDFLAGS to the /include subdirectory; you want to set it to the 
/lib subdirectory.


-Justin


Can someone help me with this?


Pooja

--
Quaerendo Invenietis-Seek and you shall discover.



--


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] Installing gromacs from git

[Sai Pooja]

I am sorry that was a typo in the mail. It was set to lib

On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul  wrote:

>
>
> Sai Pooja wrote:
>
>> Hi,
>>
>> I followed the following steps to install gromacs from the git repository:
>>
>> 1) installed git
>> 2) got a clone of gromacs using the anonymous option
>>
>> 3) installed fftw libraries using
>> ./configure --enable-float --prefix=/fs/home/sm868
>> make
>> make install
>>
>> 4)export CPPFLAGS=-I/fs/home/sm868/include
>>   export LDFLAGS=-L/fs/home/sm868/include
>>
>> 6)ran ./bootstrap
>> 7)ran ./configure --prefix=/fs/home/sm868
>> 8)I get the error - checking for sqrt in -lm... yes
>> checking for fftw3.h... yes
>> checking for main in -lfftw3f... no
>> configure: error: Cannot find fftw3f library
>>
>>
> You set your LDFLAGS to the /include subdirectory; you want to set it to
> the /lib subdirectory.
>
> -Justin
>
>
>  Can someone help me with this?
>>
>>
>> Pooja
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>>
> --
> 
>
> 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] Installing gromacs from git

[Mark Abraham]

- Original Message -
From: Sai Pooja 
Date: Sunday, June 20, 2010 9:35
Subject: Re: [gmx-users] Installing gromacs from git
To: Discussion list for GROMACS users 

> I am sorry that was a typo in the mail. It was set to lib 

That makes it hard for us to have confidence in the rest of your command lines 
- copying and pasting the results of "history" is a good way to avoid such 
problems.

As such I can only suggest looking for "error" in the last 100 lines of 
config.log and seeing what you find. That, and trying it all again :-)

Mark

> On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul  wrote:
 > 
 > 
>  Sai Pooja wrote:
 >  Hi,
 > 
>  I followed the following steps to install gromacs from the git repository:
 > 
>  1) installed git
>  2) got a clone of gromacs using the anonymous option
 > 
>  3) installed fftw libraries using
>  ./configure --enable-float --prefix=/fs/home/sm868
>  make
>  make install
 > 
>  4)export CPPFLAGS=-I/fs/home/sm868/include
> export LDFLAGS=-L/fs/home/sm868/include
 > 
>  6)ran ./bootstrap
>  7)ran ./configure --prefix=/fs/home/sm868
>  8)I get the error - checking for sqrt in -lm... yes
>  checking for fftw3.h... yes
>  checking for main in -lfftw3f... no
>  configure: error: Cannot find fftw3f library
 > 
  > 
>  You set your LDFLAGS to the /include subdirectory; you want to set it to the 
> /lib subdirectory.
 > 
>  -Justin
 > 
 >  Can someone help me with this?
 > 
 > 
>  Pooja
 > 
>  -- 
>  Quaerendo Invenietis-Seek and you shall discover.
 > 
  > 
>  -- 
>  
 > 
>  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/search before posting!
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 > 
> > 
> -- 
> Quaerendo Invenietis-Seek and you shall discover.
 > -- 
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Installing gromacs from git

[Sai Pooja]

History log:

189  ./configure --enable-threads --enable-float
--prefix=/fs/home/sm868/fftw-3.2.2
  190  make
  191  clear
  192  make install
  193  cd ..
  194  cd gromacs
  195  ls
  196  export CPPFLAGS="-I/fs/home/sm868/fftw-3.2.2/include"
  197  export LDFLAGS="-L/fs/home/sm868/fftw-3.2.2/lib"
  198  ./bootstrap
  199  ls
  200  ./configure --prefix=/fs/home/sm868/gromacs
  201  make
  202  make install

Everything works till I get the following error with make install(after it
runs for a while) :
make[3]: *** [install-man1] Error 1
make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/fs/home/sm868/gromacs/man'
make: *** [install-recursive] Error 1

Pooja










On Sat, Jun 19, 2010 at 7:49 PM, Mark Abraham wrote:

>
>
> - Original Message -
> From: Sai Pooja 
> Date: Sunday, June 20, 2010 9:35
> Subject: Re: [gmx-users] Installing gromacs from git
> To: Discussion list for GROMACS users 
>
> > I am sorry that was a typo in the mail. It was set to lib
>
> That makes it hard for us to have confidence in the rest of your command
> lines - copying and pasting the results of "history" is a good way to avoid
> such problems.
>
> As such I can only suggest looking for "error" in the last 100 lines of
> config.log and seeing what you find. That, and trying it all again :-)
>
> Mark
>
>
> > On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul wrote:
>
>> >
>> >
>> > Sai Pooja wrote:
>>
>>> > Hi,
>>> >
>>> > I followed the following steps to install gromacs from the git
>>> repository:
>>> >
>>> > 1) installed git
>>> > 2) got a clone of gromacs using the anonymous option
>>> >
>>> > 3) installed fftw libraries using
>>> > ./configure --enable-float --prefix=/fs/home/sm868
>>> > make
>>> > make install
>>> >
>>> > 4)export CPPFLAGS=-I/fs/home/sm868/include
>>> >   export LDFLAGS=-L/fs/home/sm868/include
>>> >
>>> > 6)ran ./bootstrap
>>> > 7)ran ./configure --prefix=/fs/home/sm868
>>> > 8)I get the error - checking for sqrt in -lm... yes
>>> > checking for fftw3.h... yes
>>> > checking for main in -lfftw3f... no
>>> > configure: error: Cannot find fftw3f library
>>> >
>>>
>> >
>> > You set your LDFLAGS to the /include subdirectory; you want to set it
>> to the /lib subdirectory.
>> >
>> > -Justin
>>
>> >
>>
>>> > Can someone help me with this?
>>> >
>>> >
>>> > Pooja
>>> >
>>> > --
>>> > Quaerendo Invenietis-Seek and you shall discover.
>>> >
>>>
>> >
>> > --
>> > 
>> >
>> > 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/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/mailing_lists/users.php
>>
> >
> >
> >
> > --
> > Quaerendo Invenietis-Seek and you shall discover.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Installing gromacs from git

[Mark Abraham]

- Original Message -
From: Sai Pooja 
Date: Sunday, June 20, 2010 15:09
Subject: Re: [gmx-users] Installing gromacs from git
To: Discussion list for GROMACS users 

> History log:
> 189  ./configure --enable-threads --enable-float 
> --prefix=/fs/home/sm868/fftw-3.2.2>   190  make>   191  clear>   192  make 
> install>   193  cd .. >   194  cd gromacs>   195  ls>   196  export 
> CPPFLAGS="-I/fs/home/sm868/fftw-3.2.2/include">   197  export 
> LDFLAGS="-L/fs/home/sm868/fftw-3.2.2/lib">   198  ./bootstrap >   199  ls>   
> 200  ./configure --prefix=/fs/home/sm868/gromacs>   201  make>   202  make 
> install> 
> Everything works till I get the following error with make install(after it 
> runs for a while) : > make[3]: *** [install-man1] Error 1> make[3]: Leaving 
> directory `/fs/home/sm868/gromacs/man/man1'> make[2]: *** [install-am] Error 
> 2> make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' > make[1]: 
> *** [install-recursive] Error 1> make[1]: Leaving directory 
> `/fs/home/sm868/gromacs/man'> make: *** [install-recursive] Error 1

This is just make cleaning up after recursive invocation. The actual error is 
further up. Note that if configure failed according to your previous email, 
then there's no point to using make.

Mark

> On Sat, Jun 19, 2010 at 7:49 PM, Mark Abraham  wrote:
 > 
> 
> - Original Message -
> From: Sai Pooja 
>  Date: Sunday, June 20, 2010 9:35
> Subject: Re: [gmx-users] Installing gromacs from git
> To: Discussion list for GROMACS users 
 > 
> > I am sorry that was a typo in the mail. It was set to lib 
> 
> That makes it hard for us to have confidence in the rest of your command 
> lines - copying and pasting the results of "history" is a good way to avoid 
> such problems.
 > 
> As such I can only suggest looking for "error" in the last 100 lines of 
> config.log and seeing what you find. That, and trying it all again :-)
> 
> Mark > 
> 
> > On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul  wrote:
  > > 
  > > 
> >  Sai Pooja wrote:
  > >  Hi,
  > > 
> >  I followed the following steps to install gromacs from the git repository:
  > > 
> >  1) installed git
 > >  2) got a clone of gromacs using the anonymous option
>  > 
 > >  3) installed fftw libraries using
> >  ./configure --enable-float --prefix=/fs/home/sm868
 > >  make
> >  make install
  > > 
> >  4)export CPPFLAGS=-I/fs/home/sm868/include
 > > export LDFLAGS=-L/fs/home/sm868/include
>  > 
 > >  6)ran ./bootstrap
> >  7)ran ./configure --prefix=/fs/home/sm868
 > >  8)I get the error - checking for sqrt in -lm... yes
> >  checking for fftw3.h... yes
 > >  checking for main in -lfftw3f... no
> >  configure: error: Cannot find fftw3f library
  > > 
>   > 
 > >  You set your LDFLAGS to the /include subdirectory; you want to set it to 
 > > the /lib subdirectory.
>  > 
 > >  -Justin
>  > 
  > >  Can someone help me with this?
  > > 
>  > 
 > >  Pooja
>  > 
 > >  -- 
> >  Quaerendo Invenietis-Seek and you shall discover.
  > > 
>   > 
 > >  -- 
> >  
  > > 
> >  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/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/mailing_lists/users.php
  > > 
> >  > > 
> > -- 
 > > Quaerendo Invenietis-Seek and you shall discover.
>  > -- 
> > gmx-users mailing listgmx-users@gromacs.org
>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > 
> --
>  gmx-users mailing listgmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
> 
> > 
> -- 
> Quaerendo Invenietis-Seek and you shall discover.
   > -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search 
> before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www i

Re: [gmx-users] Installing gromacs from git

[Sai Pooja]

I redid the entire thing after that first mail in which i reported the error
related to fftw(including running the make uninstall commands and removing
the folders entirely and getting fresh ones). I apologize for not specifying
this and like I said... there seemed to be no errors this time except when I
ran make install for gromacs. The error looks like this:
 make[3]: *** [install-man1] Error 1
> make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1'
> make[2]: *** [install-am] Error 2
> make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1'
> make[1]: *** [install-recursive] Error 1
> make[1]: Leaving directory `/fs/home/sm868/gromacs/man'
> make: *** [install-recursive] Error 1
I didn't find any other error.. is there a way to look for them other than
looking at what is being printed while the command is running? I tried $
grep "Error" */* in the folder but found nothing more than entries in
different scripts etc.






On Sun, Jun 20, 2010 at 1:27 AM, Mark Abraham wrote:

>
>
> - Original Message -
> From: Sai Pooja 
> Date: Sunday, June 20, 2010 15:09
> Subject: Re: [gmx-users] Installing gromacs from git
> To: Discussion list for GROMACS users 
>
> > History log:
>
> > 189  ./configure --enable-threads --enable-float
> --prefix=/fs/home/sm868/fftw-3.2.2
> >   190  make
> >   191  clear
> >   192  make install
> >   193  cd ..
> >   194  cd gromacs
> >   195  ls
> >   196  export CPPFLAGS="-I/fs/home/sm868/fftw-3.2.2/include"
> >   197  export LDFLAGS="-L/fs/home/sm868/fftw-3.2.2/lib"
> >   198  ./bootstrap
> >   199  ls
> >   200  ./configure --prefix=/fs/home/sm868/gromacs
> >   201  make
> >   202  make install
> >
> > Everything works till I get the following error with make install(after
> it runs for a while) :
> > make[3]: *** [install-man1] Error 1
> > make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1'
> > make[2]: *** [install-am] Error 2
> > make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1'
> > make[1]: *** [install-recursive] Error 1
> > make[1]: Leaving directory `/fs/home/sm868/gromacs/man'
> > make: *** [install-recursive] Error 1
>
> This is just make cleaning up after recursive invocation. The actual error
> is further up. Note that if configure failed according to your previous
> email, then there's no point to using make.
>
> Mark
>
> > On Sat, Jun 19, 2010 at 7:49 PM, Mark Abraham 
> > wrote:
>
>> >
>> >
>> > - Original Message -
>> > From: Sai Pooja 
>> > Date: Sunday, June 20, 2010 9:35
>> > Subject: Re: [gmx-users] Installing gromacs from git
>> > To: Discussion list for GROMACS users 
>> >
>> > > I am sorry that was a typo in the mail. It was set to lib
>> >
>> > That makes it hard for us to have confidence in the rest of your
>> command lines - copying and pasting the results of "history" is a good way
>> to avoid such problems.
>> >
>> > As such I can only suggest looking for "error" in the last 100 lines of
>> config.log and seeing what you find. That, and trying it all again :-)
>> >
>> > Mark
>> >
>> >
>> > > On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul wrote:
>>
>>> > >
>>> > >
>>> > > Sai Pooja wrote:
>>>
 > > Hi,
 > >
 > > I followed the following steps to install gromacs from the git
 repository:
 > >
 > > 1) installed git
 > > 2) got a clone of gromacs using the anonymous option
 > >
 > > 3) installed fftw libraries using
 > > ./configure --enable-float --prefix=/fs/home/sm868
 > > make
 > > make install
 > >
 > > 4)export CPPFLAGS=-I/fs/home/sm868/include
 > >   export LDFLAGS=-L/fs/home/sm868/include
 > >
 > > 6)ran ./bootstrap
 > > 7)ran ./configure --prefix=/fs/home/sm868
 > > 8)I get the error - checking for sqrt in -lm... yes
 > > checking for fftw3.h... yes
 > > checking for main in -lfftw3f... no
 > > configure: error: Cannot find fftw3f library
 > >
 >
>>>
>>> >
>>> > > You set your LDFLAGS to the /include subdirectory; you want to set
>>> it to the /lib subdirectory.
>>> > >
>>> > > -Justin
>>>
>>> > >
>>>
 > > Can someone help me with this?
 > >
 > >
 > > Pooja
 > >
 > > --
 > > Quaerendo Invenietis-Seek and you shall discover.
 > >
 >
>>>
>>> >
>>> > > --
>>> > > 
>>> > >
>>> > > 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/search before
>>> posti