Re: [gmx-users] Gromacs setup on dual core machine

[Jens Pohl]

Hello!

I have a similar problem with installing gromacs on a dual core machine. 
When I go through the procedure described by Matheus Fazian Ige Gondo a bit 
further down installing lam/mpi then fftw and finally gromacs everything seems 
to be working fine, but lam/mpi doesn't recognize the two cores and with mdrun 
there will be an fatal error. grompp and mdrun both were run with -np 2 and the 
output of mdrun says, that the file was made for two nodes but mdrun expected 
it to be for one node. 

With lamnodes there is only one node on cpu0 on localhost... What to do in this 
case?

Thanks in advance
Jens


>Hello Ricardo
> 
> Did you install with the sources ? (make install) ?
> Go to the folder where you ran this command and run "make uninstall"
> 
> Matheus Fazian Ige Gondo
> Departamento de Física e Biofísica
> Instituto de Biociências
> Unesp - Botucatu - SP
>  [EMAIL PROTECTED]
> +55 (14) 3811-6254
> 
> 
> On Tue, Mar 11, 2008 at 1:55 PM, Ricardo Soares <[EMAIL PROTECTED]> wrote:
>  
> 
> Kpiwara De X-nelo wrote:
> Hello
> You'll need FFTW (fftw.org) LAM/MPI (lam-mpi.org) and gromacs sources
> Download the 3 packages
> start with the Lam/MPI (configure , make ,  make install)
> Then fftw (the 2.1.5 version is needed, the 3.2 supports it but is
> still unstable) (configure --enable-mpi, make, make install)
> Then, finally, the GROMACS (configure --with-fft=fftw2 --enable-mpi ,
> make , make install)
>  
> It should be running
> as a non root user type lamboot
> It should start the lam/mpi
>  
> run your simulations as usual just changing these
> grompp -v -f xx -o xx -c xx -p xx -np
> #
>  
>  the -np generate statusfile for
> # nodes
>  
> then
>  
>  mpirun c0 C
> mdrun
> -v -s xx -o xx -e xx -c xx -g x -np
> # log >& xx
>  
>   Number of nodes (#) , must be the same as used for
> grompp
>  
> the mpirun c0 C tells it to run on the maximun available nodes.
>  
> Hope I helped.
>  
> Matheus Fazian Ige Gondo
> Departamento de Física e Biofísica
> Instituto de Biociências
> Unesp - Botucatu - SP
>  [EMAIL PROTECTED]
> +55 (14) 3811-6254
> Hello Matheus, you sure did help!
> But that way I'd need to uninstall gromacs and reinstall. Is there a
> way to include the LAM/MPI package in an already installed instance of
> Gromacs? If not, how do I uninstal it?
> 
> Thanks again!
> -- ___
> Ricardo Oliveira dos Santos Soares
> Post-graduation Student in Biological Physics
> University of Sao Paulo - USP
> Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
> Phone: 55 (16) 3602-4840
> Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
> ___
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Re: [gmx-users] Gromacs setup on dual core machine

[David van der Spoel]

Jens Pohl wrote:

Hello!

I have a similar problem with installing gromacs on a dual core machine. 
When I go through the procedure described by Matheus Fazian Ige Gondo a bit further down installing lam/mpi then fftw and finally gromacs everything seems to be working fine, but lam/mpi doesn't recognize the two cores and with mdrun there will be an fatal error. grompp and mdrun both were run with -np 2 and the output of mdrun says, that the file was made for two nodes but mdrun expected it to be for one node. 


With lamnodes there is only one node on cpu0 on localhost... What to do in this 
case?


Fetch fftw 3.1.1 (latest stable)
./configure  --enable-float
make install

Fetch openmpi 1.1.x (latest stable)
./configure
make install

Fetch gromacs
./configure --enable-mpi
make install

That's all you need



Thanks in advance
Jens



Hello Ricardo

Did you install with the sources ? (make install) ?
Go to the folder where you ran this command and run "make uninstall"

Matheus Fazian Ige Gondo
Departamento de Física e Biofísica
Instituto de Biociências
Unesp - Botucatu - SP
 [EMAIL PROTECTED]
+55 (14) 3811-6254


On Tue, Mar 11, 2008 at 1:55 PM, Ricardo Soares <[EMAIL PROTECTED]> wrote:
 


Kpiwara De X-nelo wrote:
Hello
You'll need FFTW (fftw.org) LAM/MPI (lam-mpi.org) and gromacs sources
Download the 3 packages
start with the Lam/MPI (configure , make ,  make install)
Then fftw (the 2.1.5 version is needed, the 3.2 supports it but is
still unstable) (configure --enable-mpi, make, make install)
Then, finally, the GROMACS (configure --with-fft=fftw2 --enable-mpi ,
make , make install)
 
It should be running

as a non root user type lamboot
It should start the lam/mpi
 
run your simulations as usual just changing these

grompp -v -f xx -o xx -c xx -p xx -np
#
 
 the -np generate statusfile for

# nodes
 
then
 
 mpirun c0 C

mdrun
-v -s xx -o xx -e xx -c xx -g x -np
# log >& xx
 
  Number of nodes (#) , must be the same as used for

grompp
 
the mpirun c0 C tells it to run on the maximun available nodes.
 
Hope I helped.
 
Matheus Fazian Ige Gondo

Departamento de Física e Biofísica
Instituto de Biociências
Unesp - Botucatu - SP
 [EMAIL PROTECTED]
+55 (14) 3811-6254
Hello Matheus, you sure did help!
But that way I'd need to uninstall gromacs and reinstall. Is there a
way to include the LAM/MPI package in an already installed instance of
Gromacs? If not, how do I uninstal it?

Thanks again!
-- ___
Ricardo Oliveira dos Santos Soares
Post-graduation Student in Biological Physics
University of Sao Paulo - USP
Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
Phone: 55 (16) 3602-4840
Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
___

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Re: [gmx-users] Gromacs setup on dual core machine

[Mark Abraham]

Jens Pohl wrote:

Hello!

I have a similar problem with installing gromacs on a dual core machine. 
When I go through the procedure described by Matheus Fazian Ige Gondo a bit further down installing lam/mpi then fftw and finally gromacs everything seems to be working fine, but lam/mpi doesn't recognize the two cores and with mdrun there will be an fatal error. grompp and mdrun both were run with -np 2 and the output of mdrun says, that the file was made for two nodes but mdrun expected it to be for one node. 


With lamnodes there is only one node on cpu0 on localhost... What to do in this 
case?


Read the LAM documentation to find out how to configure lam to put two 
processes on the same host. Then, restart LAM. Then use mpirun -n 2 
mdrun -n 2 and your other options.


Mark
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Re: [gmx-users] Gromacs setup on dual core machine

[Jens Pohl]

> 
> Jens Pohl wrote:
> > Hello!
> > 
> > I have a similar problem with installing gromacs on a dual core machine. 
> > When I go through the procedure described by Matheus Fazian Ige Gondo a bit 
> > further down installing lam/mpi then fftw and finally gromacs everything 
> > seems to be working fine, but lam/mpi doesn't recognize the two cores and 
> > with mdrun there will be an fatal error. grompp and mdrun both were run 
> > with -np 2 and the output of mdrun says, that the file was made for two 
> > nodes but mdrun expected it to be for one node. 
> > 
> > With lamnodes there is only one node on cpu0 on localhost... What to do in 
> > this case?
> 
> Read the LAM documentation to find out how to configure lam to put two 
> processes on the same host. Then, restart LAM. Then use mpirun -n 2 
> mdrun -n 2 and your other options.

Thank you. I hope it'll work. When I tried yesterday I couldn't find anything 
useful in the documentation until a blackout stopped me... 
Jens

> 
> Mark
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[gmx-users] results of energy minimization

[s lal badshah]

Dear gromacs experts,
I have run the energy minimization of a protein.With the tail command it shows 
the following results:
[EMAIL PROTECTED]:~/protein> tail -15 md.log
 NS-Pairs 94.365846 1981.68276620.0
 Reset In Box  0.5693855.124465 0.1
 Shift-X   0.5693103.415860 0.0
 CG-CoM0.1907855.532765 0.1
 Bonds 0.394530   16.964790 0.2
 Angles0.253320   41.291160 0.4
 Propers   0.0098552.256795 0.0
 RB-Dihedrals  0.086835   21.448245 0.2
---
 Total  9893.632954   100.0
---

   NODE (s)   Real (s)  (%)
   Time: 15.000 15.000100.0
Finished mdrun on node 0 Wed Mar 12 12:50:59 2008
I have check the em.log file, which shows the following data:

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -1.9742134e+21
Maximum force =  4.1648520e+06 on atom 1934
Norm of force =  5.6557945e+06
Is the energy minimization finished or not? when I use the top command the 
values fluctuates.As there any specific value or notation below the command 
name from which I know that energy minimization is running or finished.As in 
amber software the word sander is written below the command when check with 
"top ".Here X is written.
Regards,
Lal badshah.

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Re: [gmx-users] results of energy minimization

[Per Larsson]

Hello!

Check out
http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_change_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_precision

Cheers
/Per


12 mar 2008 kl. 11.58 skrev s lal badshah:


Dear gromacs experts,
I have run the energy minimization of a protein.With the tail  
command it shows the following results:

[EMAIL PROTECTED]:~/protein> tail -15 md.log
 NS-Pairs 94.365846 1981.68276620.0
 Reset In Box  0.5693855.124465 0.1
 Shift-X   0.5693103.415860 0.0
 CG-CoM0.1907855.532765 0.1
 Bonds 0.394530   16.964790 0.2
 Angles0.253320   41.291160 0.4
 Propers   0.0098552.256795 0.0
 RB-Dihedrals  0.086835   21.448245 0.2
---
 Total  9893.632954   100.0
---

   NODE (s)   Real (s)  (%)
   Time: 15.000 15.000100.0
Finished mdrun on node 0 Wed Mar 12 12:50:59 2008
I have check the em.log file, which shows the following data:

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -1.9742134e+21
Maximum force =  4.1648520e+06 on atom 1934
Norm of force =  5.6557945e+06
Is the energy minimization finished or not? when I use the top  
command the values fluctuates.As there any specific value or  
notation below the command name from which I know that energy  
minimization is running or finished.As in amber software the word  
sander is written below the command when check with "top ".Here X is  
written.

Regards,
Lal badshah.
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[gmx-users] How to judge the system was equilibrated

[Rui Li]

Dear all!

I ran a simulation of a ligand bound to an enzyme,and I want know when the 
system
achieved equilibration. Can I judge it from rmsd or potential?
Which rmsd should I obtained? the backbone protein or the drug ligand?

Thanks in advance!


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Re: [gmx-users] results of energy minimization

[Justin A. Lemkul]

Quoting s lal badshah <[EMAIL PROTECTED]>:

> Dear gromacs experts,
> I have run the energy minimization of a protein.With the tail command it
> shows the following results:
> [EMAIL PROTECTED]:~/protein> tail -15 md.log
>  NS-Pairs 94.365846 1981.68276620.0
>  Reset In Box  0.5693855.124465 0.1
>  Shift-X   0.5693103.415860 0.0
>  CG-CoM0.1907855.532765 0.1
>  Bonds 0.394530   16.964790 0.2
>  Angles0.253320   41.291160 0.4
>  Propers   0.0098552.256795 0.0
>  RB-Dihedrals  0.086835   21.448245 0.2
> ---
>  Total  9893.632954   100.0
> ---
>
>NODE (s)   Real (s)  (%)
>Time: 15.000 15.000100.0
> Finished mdrun on node 0 Wed Mar 12 12:50:59 2008
> I have check the em.log file, which shows the following data:
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -1.9742134e+21
> Maximum force =  4.1648520e+06 on atom 1934
> Norm of force =  5.6557945e+06
> Is the energy minimization finished or not? when I use the top command the
> values fluctuates.As there any specific value or notation below the command

EM is finished, hence the line in your md.log file that tells you "Finished
mdrun..."  Using the top command, you will undoubtedly see lots of things
fluctuating, as there are (hopefully) several processes on your machine that
are keeping it working.  What you are looking for is "mdrun," which, as I said,
should have finished.

You will also note that mdrun is telling you that it "converged to machine
precision," which means the algorithm has reached a satisfactory end, within
the limits of your hardware.

-Justin

> name from which I know that energy minimization is running or finished.As in
> amber software the word sander is written below the command when check with
> "top ".Here X is written.
> Regards,
> Lal badshah.
>
>  Send instant messages to your online friends http://uk.messenger.yahoo.com





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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[gmx-users] DMSO G53a6 FF in Gromacs

[Andreas Boozo Frank]

Dear Gromacs Users,

I simulated the preequilibrated box of DMSO that is located in the 
Gromacs Force Field Distribution with the G53a6 Gromos FF parameters 
(adapted from the Geerke et. al paper in J Phys Chem B, 108 (2004)). 
After temperature equilibration I performed a NPT run but in contrast to 
the reported density of 1095 kg m-3 I always get values around 1108 kg 
m-3. I used berendsen pressure coupling as well as reaction field for 
treating long-range interactions with 0.8 / 1.4 cut-offs.
I looked through the  Gromacs archive but couldnt find an answer for 
this problem. Has anyone an idea what could be the reason for this result?


Thanks for any comments!

Best regards,

Andreas
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Re[3]: [gmx-users] size of the system

[V.V. Chaban]

> The correct file to use is spc216.gro (which genbox automatically finds in
> the GROMACS $GMXLIB/top directory). I'm guessing that genbox is finding a
> local spc216.pdb which is somehow broken.
Thanks a lot. I've fixed the problem translating ".pdb" to ".gro"
It was really something wrong with .pdb although there was ".pdb" from
GROMACS folder.

-- 
Vitaly Chaban
University of Kharkiv
Svobody sq.,4
Kharkiv 61077, Ukraine

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[gmx-users] Re: DMSO G53a6 FF in Gromacs

[Andreas Boozo Frank]

Hi Berk,

Thanks for replying so quick. I made it rigid in that way that I used 
bonded interactions also for the groups that are not directly connected 
(FF parameters gb_49 & gb_50) and then applied all-bond SHAKE. For the 
other bonds I used gb_41, gb42 and for the three angles ga_45 and ga_46.


Andreas
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RE: [gmx-users] DMSO G53a6 FF in Gromacs

[Berk Hess]

Hi,

Did you make your DMSO molecule completely rigid?

Berk.

> Date: Wed, 12 Mar 2008 12:18:08 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] DMSO G53a6 FF in Gromacs
> 
> Dear Gromacs Users,
> 
> I simulated the preequilibrated box of DMSO that is located in the 
> Gromacs Force Field Distribution with the G53a6 Gromos FF parameters 
> (adapted from the Geerke et. al paper in J Phys Chem B, 108 (2004)). 
> After temperature equilibration I performed a NPT run but in contrast to 
> the reported density of 1095 kg m-3 I always get values around 1108 kg 
> m-3. I used berendsen pressure coupling as well as reaction field for 
> treating long-range interactions with 0.8 / 1.4 cut-offs.
> I looked through the  Gromacs archive but couldnt find an answer for 
> this problem. Has anyone an idea what could be the reason for this result?
> 
> Thanks for any comments!
> 
> Best regards,
> 
> Andreas
> -- 
> 
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Re: [gmx-users] DMSO G53a6 FF in Gromacs

[Xavier Periole]

On Wed, 12 Mar 2008 12:24:02 +0100
 Berk Hess <[EMAIL PROTECTED]> wrote:

Hi,

Did you make your DMSO molecule completely rigid?


Should we really worry about such a difference in density?
(1095-1108)/1095=0.012

How precise is the value reported? Did you estimate the error
by using different sections of the trajectory?


Berk.


Date: Wed, 12 Mar 2008 12:18:08 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] DMSO G53a6 FF in Gromacs

Dear Gromacs Users,

I simulated the preequilibrated box of DMSO that is located in the 
Gromacs Force Field Distribution with the G53a6 Gromos FF parameters 
(adapted from the Geerke et. al paper in J Phys Chem B, 108 (2004)). 
After temperature equilibration I performed a NPT run but in contrast to 
the reported density of 1095 kg m-3 I always get values around 1108 kg 
m-3. I used berendsen pressure coupling as well as reaction field for 
treating long-range interactions with 0.8 / 1.4 cut-offs.
I looked through the  Gromacs archive but couldnt find an answer for 
this problem. Has anyone an idea what could be the reason for this result?


Thanks for any comments!

Best regards,

Andreas
--

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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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Re: [gmx-users] DMSO G53a6 FF in Gromacs

[Andreas Boozo Frank]

First thanks for the answers. I checked several sections of the 
trajectory, but the deviation is always the same, even when disregarding 
the first 500 ps or looking only at the last 500 ps of the trajectory 
where everything is nice equilibrated. I think the error is 
insignificantly small (however, the value was reported in this precision 
in the original paper) but I was interested in possible reasons of this 
behavour, e.g. numerical errors or different treatment of certain  
interaction parameters between Gromacs and Gromos (in my studies I 
usually work with both programs).


There is another question that could possibly be answered by Berk: I 
often use his Orientation Restraints algorithm implemented in Gromacs. 
While all results are fine and most of the analysis parameters of an 
RDC- driven run are clear to me, I am not sure of the meaning of the 
g_energy output "Orient.-Rest." and "Ori.-R.-RMSD". Are these analysis 
parameters some kind of energy terms like the
restraining potential or is the output given in Hertz and what do they 
actually mean?


Thanks in advance for any help,

Andreas



Xavier Periole wrote:


On Wed, 12 Mar 2008 12:24:02 +0100
 Berk Hess <[EMAIL PROTECTED]> wrote:


Hi,

Did you make your DMSO molecule completely rigid?


Should we really worry about such a difference in density?
(1095-1108)/1095=0.012

How precise is the value reported? Did you estimate the error
by using different sections of the trajectory?


Berk.


Date: Wed, 12 Mar 2008 12:18:08 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] DMSO G53a6 FF in Gromacs

Dear Gromacs Users,

I simulated the preequilibrated box of DMSO that is located in the 
Gromacs Force Field Distribution with the G53a6 Gromos FF parameters 
(adapted from the Geerke et. al paper in J Phys Chem B, 108 (2004)). 
After temperature equilibration I performed a NPT run but in 
contrast to the reported density of 1095 kg m-3 I always get values 
around 1108 kg m-3. I used berendsen pressure coupling as well as 
reaction field for treating long-range interactions with 0.8 / 1.4 
cut-offs.
I looked through the  Gromacs archive but couldnt find an answer for 
this problem. Has anyone an idea what could be the reason for this 
result?


Thanks for any comments!

Best regards,

Andreas
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The Netherlands
http://md.chem.rug.nl/~periole
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Re: [gmx-users] Re: DMSO G53a6 FF in Gromacs

[Andreas Boozo Frank]

Hi Berk,

I used weak berendsen temperature coupling with tau_t = 0.1 and a ref_t 
of 298.15 K. My average temperature during the NPT run (disregarding the 
first 100 ps) is ca. 298.20 K (as given by g_energy).
I had another question to you, Berk, in my last mail to the list maybe 
two hours ago, regarding your Orientation Restraints algorithm. Have you 
seen this or should I repost it?


Best regards,

Andreas


Berk Hess wrote:







> Date: Wed, 12 Mar 2008 12:31:12 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: DMSO G53a6 FF in Gromacs
>
> Hi Berk,
>
> Thanks for replying so quick. I made it rigid in that way that I used
> bonded interactions also for the groups that are not directly connected
> (FF parameters gb_49 & gb_50) and then applied all-bond SHAKE. For the
> other bonds I used gb_41, gb42 and for the three angles ga_45 and ga_46.
>
> Andreas

There could be another issue.
With reaction-field you always introduce integration errors.
With water this leads to a temperature of 305 K when Berendsen coupling
to 300 K with tau_t=0.1 ps and the Gromos cut-off setup.

In Gromos there is/was a problem with inconsistent ways of determining
the temperature. Therefore the effective temperature in the simulation
can be several degrees higher than the one reported in the paper.

What coupling method did you use and what is your real temperature?

Berk.



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RE: [gmx-users] Re: DMSO G53a6 FF in Gromacs

[Berk Hess]

> Date: Wed, 12 Mar 2008 12:31:12 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: DMSO G53a6 FF in Gromacs
> 
> Hi Berk,
> 
> Thanks for replying so quick. I made it rigid in that way that I used 
> bonded interactions also for the groups that are not directly connected 
> (FF parameters gb_49 & gb_50) and then applied all-bond SHAKE. For the 
> other bonds I used gb_41, gb42 and for the three angles ga_45 and ga_46.
> 
> Andreas

There could be another issue.
With reaction-field you always introduce integration errors.
With water this leads to a temperature of 305 K when Berendsen coupling
to 300 K with tau_t=0.1 ps and the Gromos cut-off setup.

In Gromos there is/was a problem with inconsistent ways of determining
the temperature. Therefore the effective temperature in the simulation
can be several degrees higher than the one reported in the paper.

What coupling method did you use and what is your real temperature?

Berk.


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[gmx-users] orires energy terms

[Berk Hess]

Hi,

"Orient.-Rest." is the potential energy of the restraints (in kJ/mol).
"Ori.-R.-RMSD" is the RMS deviation of the orientations in units of your 
orientation
observable input.

Berk.

> 
> There is another question that could possibly be answered by Berk: I 
> often use his Orientation Restraints algorithm implemented in Gromacs. 
> While all results are fine and most of the analysis parameters of an 
> RDC- driven run are clear to me, I am not sure of the meaning of the 
> g_energy output "Orient.-Rest." and "Ori.-R.-RMSD". Are these analysis 
> parameters some kind of energy terms like the
> restraining potential or is the output given in Hertz and what do they 
> actually mean?
> 
> Thanks in advance for any help,
> 
> Andreas
> 
> 
> 
> Xavier Periole wrote:
> 
> > On Wed, 12 Mar 2008 12:24:02 +0100
> >  Berk Hess <[EMAIL PROTECTED]> wrote:
> >
> >> Hi,
> >>
> >> Did you make your DMSO molecule completely rigid?
> >>
> > Should we really worry about such a difference in density?
> > (1095-1108)/1095=0.012
> >
> > How precise is the value reported? Did you estimate the error
> > by using different sections of the trajectory?
> >
> >> Berk.
> >>
> >>> Date: Wed, 12 Mar 2008 12:18:08 +0100
> >>> From: [EMAIL PROTECTED]
> >>> To: gmx-users@gromacs.org
> >>> Subject: [gmx-users] DMSO G53a6 FF in Gromacs
> >>>
> >>> Dear Gromacs Users,
> >>>
> >>> I simulated the preequilibrated box of DMSO that is located in the 
> >>> Gromacs Force Field Distribution with the G53a6 Gromos FF parameters 
> >>> (adapted from the Geerke et. al paper in J Phys Chem B, 108 (2004)). 
> >>> After temperature equilibration I performed a NPT run but in 
> >>> contrast to the reported density of 1095 kg m-3 I always get values 
> >>> around 1108 kg m-3. I used berendsen pressure coupling as well as 
> >>> reaction field for treating long-range interactions with 0.8 / 1.4 
> >>> cut-offs.
> >>> I looked through the  Gromacs archive but couldnt find an answer for 
> >>> this problem. Has anyone an idea what could be the reason for this 
> >>> result?
> >>>
> >>> Thanks for any comments!
> >>>
> >>> Best regards,
> >>>
> >>> Andreas
> >>> -- 
> >>>
> >>> ___
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>> Please search the archive at http://www.gromacs.org/search before 
> >>> posting!
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> >>
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> >
> > -
> > XAvier Periole - PhD
> >
> > NMR & Molecular Dynamics Group
> > University of Groningen
> > The Netherlands
> > http://md.chem.rug.nl/~periole
> > -
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] RE: Coul-14, LJ-14 and RF-excl definitions (2)

[pascal . baillod]

Dear developers,

I would again like to thank David, Xavier and Berk for their very informative
explanations on RF-excl and 1-4 interactions. I am still a bit confused, though,
with Berk's very last statement on this issue. If I quote it:

"The reaction field is not applied to pair (1-4) terms. Therefore there are no
issues with fudgeQQ."

As far as I understood, the reaction field correction IS applied to (1-4) pairs,
but added to the RF-excl term, and not to Coul-14 term. At least this is what I
understood from another explanation from Berk, sent on the mailing list sometime
around September 2007:

"The reaction-field correction applies to ALL atom pairs that are within the
cut-off distance(or more accurately: atom pairs for which their charge group
centers are within the cutoff distance). So all "noraml non-bonded interaction
pairs, as well as all excluded pairs including self -pairs. The only issue is to
which energy term wich contribution is added. In old Gromacs versions the RF
correction for 1-4 pairs was added to the 1-4 energy term. In the newer version
its added to the RF-excl term."


I would also like understand why the reaction field correction is applied to
excluded atom pairs. The corrected coulomb potential described in the manual
reads (please open the attached pdf for the compiled equations):

V_{crf} = f *q_i *q_j [ \frac{1}{r_{ij}} + k_{rf}r^2_{ij} - c_{rf} ] (1)

This is equivalent to

V_{crf} = V_c  + V_{rf} (2)

where V_c is the usual Coulomb potential energy, and V_{rf} is the  
reaction field correction.

For excluded atom pairs, there is no Coulomb interaction, except for 1-4 pairs,
where there is a reduced Coulomb interaction. However, in agreement with what I
state above, the code dose seem to compute a reaction field correction for all
excluded atom pairs. In the RF_excl_correction routine of mdlib/rf_util.c, this
correction reads:

V_{rf} = f q_i  q_j   ( k_{rf}r^2_{ij} - c_{rf} )

That means we apply a potential that is a function of r^2, yielding a force
whose magnitude increses with r and whose direction is opposed to the Coulomb
force !!! What is the physical justification to V_{rf}  in the absence of V_c
for excluded pairs?

I thank you very much for your help!

Pascal


***
Pascal Baillod (PhD student) 
***
Swiss Federal Institute of Technology EPFL  Tel: +41-(0)21-693-0322
Institute of Chemical Sciences and Engineering ,Fax: +41-(0)21-693-0320
Laboratory of Computational Chemistry and Biochemistry  [EMAIL PROTECTED]
Room BCH 4121, Avenue Forel,http://lcbcpc21.epfl.ch
CH-1015 Lausanne
***


eqRF.pdf
Description: Adobe PDF document
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RE: [gmx-users] RE: Coul-14, LJ-14 and RF-excl definitions (2)

[Berk Hess]

Hi,

The RF correction is NOT applied to 1-4 pairs.
It is applied to excluded pairs, independently of it they interact via 1-4 
interaction or not.
For RF simply all atom pairs in a cut-off sphere need to be corrected.
The simplest way of doing this is correcting the non-bonded potential
and correcting all pairs that do not interact via the non-bonded potential 
(excluded pairs).

For why one has to correct all pairs with an r^2 function, you have to read the 
literature.

Berk.

> To: gmx-users@gromacs.org
> Date: Wed, 12 Mar 2008 16:26:05 +0100
> From: [EMAIL PROTECTED]
> Subject: [gmx-users] RE: Coul-14, LJ-14 and RF-excl definitions (2)
> 
> Dear developers,
> 
> I would again like to thank David, Xavier and Berk for their very informative
> explanations on RF-excl and 1-4 interactions. I am still a bit confused, 
> though,
> with Berk's very last statement on this issue. If I quote it:
> 
> "The reaction field is not applied to pair (1-4) terms. Therefore there are no
> issues with fudgeQQ."
> 
> As far as I understood, the reaction field correction IS applied to (1-4) 
> pairs,
> but added to the RF-excl term, and not to Coul-14 term. At least this is what 
> I
> understood from another explanation from Berk, sent on the mailing list 
> sometime
> around September 2007:
> 
> "The reaction-field correction applies to ALL atom pairs that are within the
> cut-off distance(or more accurately: atom pairs for which their charge group
> centers are within the cutoff distance). So all "noraml non-bonded interaction
> pairs, as well as all excluded pairs including self -pairs. The only issue is 
> to
> which energy term wich contribution is added. In old Gromacs versions the RF
> correction for 1-4 pairs was added to the 1-4 energy term. In the newer 
> version
> its added to the RF-excl term."
> 
> 
> I would also like understand why the reaction field correction is applied to
> excluded atom pairs. The corrected coulomb potential described in the manual
> reads (please open the attached pdf for the compiled equations):
> 
> V_{crf} = f *q_i *q_j [ \frac{1}{r_{ij}} + k_{rf}r^2_{ij} - c_{rf} ] (1)
> 
> This is equivalent to
> 
> V_{crf} = V_c  + V_{rf} (2)
> 
> where V_c is the usual Coulomb potential energy, and V_{rf} is the  
> reaction field correction.
> 
> For excluded atom pairs, there is no Coulomb interaction, except for 1-4 
> pairs,
> where there is a reduced Coulomb interaction. However, in agreement with what 
> I
> state above, the code dose seem to compute a reaction field correction for all
> excluded atom pairs. In the RF_excl_correction routine of mdlib/rf_util.c, 
> this
> correction reads:
> 
> V_{rf} = f q_i  q_j   ( k_{rf}r^2_{ij} - c_{rf} )
> 
> That means we apply a potential that is a function of r^2, yielding a force
> whose magnitude increses with r and whose direction is opposed to the Coulomb
> force !!! What is the physical justification to V_{rf}  in the absence of V_c
> for excluded pairs?
> 
> I thank you very much for your help!
> 
> Pascal
> 
> 
> ***
> Pascal Baillod (PhD student) 
> ***
> Swiss Federal Institute of Technology EPFLTel: +41-(0)21-693-0322
> Institute of Chemical Sciences and Engineering ,  Fax: +41-(0)21-693-0320
> Laboratory of Computational Chemistry and Biochemistry[EMAIL 
> PROTECTED]
> Room BCH 4121, Avenue Forel,  http://lcbcpc21.epfl.ch
> CH-1015 Lausanne  
> ***

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Re: [gmx-users] Re: DMSO G53a6 FF in Gromacs

[Andreas Boozo Frank]

Dear all,

I think I found the reason for the deviation after "hunderds of small 
runs"...:-): I normally used Dispersion Correction for both the energy 
and pressure because in the manual the following is noted:


"...The pressure correction in contrast is very large and can not be 
neglected. Although it is in principle possible to
parameterize a force field such that the pressure is close to 1 bar even 
without correction, such a method makes
the parameterization dependent on the cut-off and is therefore 
undesirable. Please note that it is not consistent to
use the long range correction to the dispersion without using either a 
reaction field method or a proper long range

electrostatics method such as Ewald summation or PPPM."

Maybe I got it wrong (and I am still a little bit confused) but because 
I used the reaction-field approximation I turned on DispCorr for 
Pressure. However, it seems that the Gromos DMSO FF was established in a 
way that the correction is "included" in the parameter set which was / 
is not clear to me when reading the DMSO paper.


And thank you Berk for the explanation of the Orire parameters.

CU,

Andreas


Berk Hess wrote:







> Date: Wed, 12 Mar 2008 12:31:12 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: DMSO G53a6 FF in Gromacs
>
> Hi Berk,
>
> Thanks for replying so quick. I made it rigid in that way that I used
> bonded interactions also for the groups that are not directly connected
> (FF parameters gb_49 & gb_50) and then applied all-bond SHAKE. For the
> other bonds I used gb_41, gb42 and for the three angles ga_45 and ga_46.
>
> Andreas

There could be another issue.
With reaction-field you always introduce integration errors.
With water this leads to a temperature of 305 K when Berendsen coupling
to 300 K with tau_t=0.1 ps and the Gromos cut-off setup.

In Gromos there is/was a problem with inconsistent ways of determining
the temperature. Therefore the effective temperature in the simulation
can be several degrees higher than the one reported in the paper.

What coupling method did you use and what is your real temperature?

Berk.



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RE: [gmx-users] Re: DMSO G53a6 FF in Gromacs

[Berk Hess]

> Date: Wed, 12 Mar 2008 17:20:19 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Re: DMSO G53a6 FF in Gromacs
> 
> Dear all,
> 
> I think I found the reason for the deviation after "hunderds of small 
> runs"...:-): I normally used Dispersion Correction for both the energy 
> and pressure because in the manual the following is noted:
> 
> "...The pressure correction in contrast is very large and can not be 
> neglected. Although it is in principle possible to
> parameterize a force field such that the pressure is close to 1 bar even 
> without correction, such a method makes
> the parameterization dependent on the cut-off and is therefore 
> undesirable. Please note that it is not consistent to
> use the long range correction to the dispersion without using either a 
> reaction field method or a proper long range
> electrostatics method such as Ewald summation or PPPM."
> 
> Maybe I got it wrong (and I am still a little bit confused) but because 
> I used the reaction-field approximation I turned on DispCorr for 
> Pressure. However, it seems that the Gromos DMSO FF was established in a 
> way that the correction is "included" in the parameter set which was / 
> is not clear to me when reading the DMSO paper.

Reaction-field is for electrostatics and has nothing to do with dispersion 
correction,
which is for Van der Waals interactions.

Gromos force fields never use a dispersion correction.

Berk.


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Re: [gmx-users] problem with mpi configuration.

[mario ciappy]

 Thank you very much for help me.
  I have try to install gromacs 3.3.3 on rhel 4.0.
  I try to configure gromacs single with the command  "./configure --enable-mpi 
--program-suffix=_mpi--prefix=/usr/local/gromacs332", but when I try to 
install, I have this error:
  usr/bin/install: cannot create regular file 
`/usr/local/gromacs/bin/grompp_mpi_d--prefix=/usr/local/gromacs333': No such 
file or directory
  make[3]: *** [install-binPROGRAMS] Error 1
  make[3]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'
  make[2]: *** [install-am] Error 2
  make[2]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'
  make[1]: *** [install-recursive] Error 1
  make[1]: Leaving directory `/home/mario/gromacs-3.3.3/src'
  make: *** [install-recursive] Error 1
  I have try to edit the end of the configure command "/usr/local/gromacs332" 
with"/usr/local/gromacs333" and "/usr/local/gromacs" but I have anlogue errors. 
Can you help me?
  
  Thanks in advance.
  
  Mario
Diego Enry <[EMAIL PROTECTED]> ha scritto: You should check the user guide.
http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?s=docs

In a nutshell:
1) You need is to install mpich in all machines. Actually you can sync
the mpich install directory (also gromacs).
2) You also need to have the same /etc/hosts on every machine. rsync that.
3) You need to grant ssh access without password by creating a rsa-key
for every user

Fell free to private message if you need any additional help.

Ciao.

On Tue, Mar 4, 2008 at 6:04 AM, mario ciappy  wrote:
> Thank's Diego,
> I'm grateful to you. I have only one question. How can I  configure mpi/lam
> for relaize the comunication between nodes?
> I have created an hostsfile with my ip addresses.
> Thank's a lot in advance.
>
> Mario
>
> Diego Enry  ha scritto:
>
>  Since you didn't show us the problems you met.. try following this:
>
> #1) Download essential packages
> #1.1) mpich
> wget
> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/mpich2-1.0.6p1.tar.gz
>
> #1.2) fftw
> wget ftp://ftp.fftw.org/pub/fftw/fftw-3.1.2.tar.gz
>
> #1.3) gromacs
> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz
>
>
> #2) compile packages:
>
> #2.1) mpich
> tar xvfz mpich2-1.0.6p1.tar.gz
> cd mpich2-1.0.6p1
> make distclean
> ./configure --with-device=ch3:nemesis --enable-fast --disable-cxx
> --enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3
> make
> make install
> make distclean
> cd ..
>
> #2.2) fftw single
> tar xvfz fftw-3.1.2.tar.gz
> cd fftw-3.1.2
> make distclean
> ./configure --enable-float --enable-sse --enable-threads
> make
> make install
> make distclean
> cd ..
>
> #2.3) gromacs single
> tar xvfz gromacs-3.3.2.tar.gz
> cd gromacs-3.3.2
> ./configure --enable-mpi --program-suffix=_mpi
> --prefix=/usr/local/gromacs332
> make
> make install
> make links
> make distclean
> cd ..
>
> #2.4) fftw double
> cd fftw-3.1.2
> ./configure --enable-sse2 --enable-threads
> make
> make install
> make distclean
> cd ..
>
> #2.2) gromacs double
> cd gromacs-3.3.2
> ./configure --enable-mpi --program-suffix=_mpi_d
> --prefix=/usr/local/gromacs332 --enable-double
> make
> make install
> make links
> make distclean
> cd ..
>
>
>
>
> On Mon, Mar 3, 2008 at 3:09 PM, mario ciappy wrote:
> > Dear all,
> > I'm tried to configure gromacs in parallel but I have meet some problems.
> > I don't understand if the problems are relative to mpi or gromacs
> > configuration. For this reason I'd be grateful if you explained a detailed
> > installation procedure of all that require to run gromacs in parallel,
> > started by mpi/lam configuration. I now that is an hard and demanding
> > request, but it is a big help for me because you are only resource.
> >
> > Thank's in advance
> >
> > Mario
> >
> >
> > 
> > 
> >
> > L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail
> > ___
> > gmx-users mailing list gmx-users@gromacs.org
> > http://www.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 [EMAIL PROTECTED]
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Diego Enry B. Gomes
> Laboratório de Modelagem e Dinamica Molecular
> Universidade Federal do Rio de Janeiro - Brasil.
> ___
> gmx-users mailing list gmx-users@gromacs.org
> http://www.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 [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
>  
> 
> L'email della prossima gene

[gmx-users] trjconv output at a specified time

[Liu Shiyong]

Hi,

I want to output a structure in a given time, for example , in step 1 during
minimization.

I tried the following command using dump:
trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb  -s
r-l_1_oplsaa.input.tpr  -t0 0 -dump 1

But It didnot work.

Output msg:

Select a group: 2
Selected 2: 'Protein-H'
trn version: GMX_trn_file (single precision)
Reading frame   0 time  125.000
Back Off! I just backed up m.pdb to ./#m.pdb.1#
Last frame 19 time 2418.000

WARNING no output, trajectory ended at 2418


gcq#76: "Baseball Heroes Only" (P.J. Harvey)

Best

-- 
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
___
gmx-users mailing listgmx-users@gromacs.org
http://www.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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] trjconv output at a specified time

[Alan Dodd]

You asked for the frame at 1ps.  The trajectory starts at 125ps, so 
unsurprisingly the program does not give you an output.


- Original Message 
From: Liu Shiyong <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users 
Sent: Wednesday, March 12, 2008 10:07:17 PM
Subject: [gmx-users] trjconv output at a specified time

Hi, 

I want to output a structure in a given time, for example , in step 1 during 
minimization.

I tried the following command using dump:
trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb  -s 
r-l_1_oplsaa.input.tpr  -t0 0 -dump 1 

But It didnot work.

Output msg:

Select a group: 2
Selected 2: 'Protein-H'
trn version: GMX_trn_file (single precision)
Reading frame   0 time  125.000
Back Off! I just backed up m.pdb to ./#m.pdb.1#
Last frame 19 time 2418.000

WARNING no output, trajectory ended at 2418


gcq#76: "Baseball Heroes Only" (P.J. Harvey)

Best

-- 
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962


-Inline Attachment Follows-

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Re: [gmx-users] trjconv output at a specified time

[Liu Shiyong]

Thanks.

The trajectory starts at 125ps ?

So  step 1  == 125 ps
  step 2 ==   250 ps
  step 3  ==  375 ps

Where is 125ps from ?

But

; RUN CONTROL PARAMETERS
integrator   = steep
; Start time and timestep in ps
tinit= 0
dt   = 0.002



On Wed, Mar 12, 2008 at 5:32 PM, Alan Dodd <[EMAIL PROTECTED]> wrote:

> You asked for the frame at 1ps.  The trajectory starts at 125ps, so
> unsurprisingly the program does not give you an output.
>
> - Original Message 
> From: Liu Shiyong <[EMAIL PROTECTED]>
> To: Discussion list for GROMACS users 
> Sent: Wednesday, March 12, 2008 10:07:17 PM
> Subject: [gmx-users] trjconv output at a specified time
>
> Hi,
>
> I want to output a structure in a given time, for example , in step 1
> during minimization.
>
> I tried the following command using dump:
> trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb  -s
> r-l_1_oplsaa.input.tpr  -t0 0 -dump 1
>
> But It didnot work.
>
> Output msg:
>
> Select a group: 2
> Selected 2: 'Protein-H'
> trn version: GMX_trn_file (single precision)
> Reading frame   0 time  125.000
> Back Off! I just backed up m.pdb to ./#m.pdb.1#
> Last frame 19 time 2418.000
>
> WARNING no output, trajectory ended at 2418
>
>
> gcq#76: "Baseball Heroes Only" (P.J. Harvey)
>
> Best
>
> --
> Shiyong Liu
> Research Assistant
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
> Homepage: http://www.people.ku.edu/~syliu
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
>
>
> -Inline Attachment Follows-
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.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 [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> __
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.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 [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
___
gmx-users mailing listgmx-users@gromacs.org
http://www.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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] problem with mpi configuration.

[Diego Enry]

/usr/local/gromacs/bin/grompp_mpi_d--prefix=/usr/local/gromacs333
<<= just zoom in the middle of the command

right here:

mpi_d--prefix=

 you forgot to put a space between "mpi_d" and "--prefix"

copy&paste the corrected version bellow.
./configure --enable-mpi --program-suffix=_mpi --prefix=/usr/local/gromacs332

have fun !


On Wed, Mar 12, 2008 at 4:05 PM, mario ciappy <[EMAIL PROTECTED]> wrote:
>
>  Thank you very much for help me.
>  I have try to install gromacs 3.3.3 on rhel 4.0.
>  I try to configure gromacs single with the command  "./configure
> --enable-mpi --program-suffix=_mpi--prefix=/usr/local/gromacs332", but when
> I try to install, I have this error:
>  usr/bin/install: cannot create regular file
> `/usr/local/gromacs/bin/grompp_mpi_d--prefix=/usr/local/gromacs333': No such
> file or directory
>  make[3]: *** [install-binPROGRAMS] Error 1
>  make[3]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'
>  make[2]: *** [install-am] Error 2
>  make[2]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'
>  make[1]: *** [install-recursive] Error 1
>  make[1]: Leaving directory `/home/mario/gromacs-3.3.3/src'
>  make: *** [install-recursive] Error 1
>  I have try to edit the end of the configure command "/usr/local/gromacs332"
> with"/usr/local/gromacs333" and "/usr/local/gromacs" but I have anlogue
> errors. Can you help me?
>
>  Thanks in advance.
>
>
>  Mario
> Diego Enry <[EMAIL PROTECTED]> ha scritto:
>  You should check the user guide.
> http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?s=docs
>
> In a nutshell:
> 1) You need is to install mpich in all machines. Actually you can sync
> the mpich install directory (also gromacs).
> 2) You also need to have the same /etc/hosts on every machine. rsync that.
> 3) You need to grant ssh access without password by creating a rsa-key
> for every user
>
> Fell free to private message if you need any additional help.
>
> Ciao.
>
> On Tue, Mar 4, 2008 at 6:04 AM, mario ciappy wrote:
> > Thank's Diego,
> > I'm grateful to you. I have only one question. How can I configure mpi/lam
> > for relaize the comunication between nodes?
> > I have created an hostsfile with my ip addresses.
> > Thank's a lot in advance.
> >
> > Mario
> >
> > Diego Enry ha scritto:
>
>
> >
> > Since you didn't show us the problems you met.. try following this:
> >
> > #1) Download essential packages
> > #1.1) mpich
> > wget
> >
> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/mpich2-1.0.6p1.tar.gz
> >
> > #1.2) fftw
> > wget ftp://ftp.fftw.org/pub/fftw/fftw-3.1.2.tar.gz
> >
> > #1.3) gromacs
> > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz
> >
> >
> > #2) compile packages:
> >
> > #2.1) mpich
> > tar xvfz mpich2-1.0.6p1.tar.gz
> > cd mpich2-1.0.6p1
> > make distclean
> > ./configure --with-device=ch3:nemesis --enable-fast --disable-cxx
> > --enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3
> > make
> > make install
> > make distclean
> > cd ..
> >
> > #2.2) fftw single
> > tar xvfz fftw-3.1.2.tar.gz
> > cd fftw-3.1.2
> > make distclean
> > ./configure --enable-float --enable-sse --enable-threads
> > make
> > make install
> > make distclean
> > cd ..
> >
> > #2.3) gromacs single
> > tar xvfz gromacs-3.3.2.tar.gz
> > cd gromacs-3.3.2
> > ./configure --enable-mpi --program-suffix=_mpi
> > --prefix=/usr/local/gromacs332
> > make
> > make install
> > make links
> > make distclean
> > cd ..
> >
> > #2.4) fftw double
> > cd fftw-3.1.2
> > ./configure --enable-sse2 --enable-threads
> > make
> > make install
> > make distclean
> > cd ..
> >
> > #2.2) gromacs double
> > cd gromacs-3.3.2
> > ./configure --enable-mpi --program-suffix=_mpi_d
> > --prefix=/usr/local/gromacs332 --enable-double
> > make
> > make install
> > make links
> > make distclean
> > cd ..
> >
> >
> >
> >
> > On Mon, Mar 3, 2008 at 3:09 PM, mario ciappy wrote:
> > > Dear all,
> > > I'm tried to configure gromacs in parallel but I have meet some
> problems.
> > > I don't understand if the problems are relative to mpi or gromacs
> > > configuration. For this reason I'd be grateful if you explained a
> detailed
> > > installation procedure of all that require to run gromacs in parallel,
> > > started by mpi/lam configuration. I now that is an hard and demanding
> > > request, but it is a big help for me because you are only resource.
> > >
> > > Thank's in advance
> > >
> > > Mario
> > >
> > >
> > > 
> > > 
> > >
> > > L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail
> > > ___
> > > gmx-users mailing list gmx-users@gromacs.org
> > > http://www.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 [EMAIL PROTECTED]
> > > Can't post? Read http://www.gromacs.org/m

Re: [gmx-users] trjconv output at a specified time

[Alan Dodd]

Select a group: 2
Selected 2: 'Protein-H'
trn version: GMX_trn_file (single precision)
Reading frame   0 time  125.000

'nuff said.  Couldn't comment on the time between frames in your file.  gmxdump 
will tell you, or get it from (nstxout or nstxtcout)*dt in your mdp.



- Original Message 
From: Liu Shiyong <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users 
Sent: Wednesday, March 12, 2008 11:24:00 PM
Subject: Re: [gmx-users] trjconv output at a specified time

Thanks.

The trajectory starts at 125ps ?

So  step 1  == 125 ps 
  step 2 ==   250 ps 
  step 3  ==  375 ps  

Where is 125ps from ?

But 

; RUN CONTROL PARAMETERS
integrator   = steep
; Start time and timestep in ps
tinit= 0
dt   = 0.002




On Wed, Mar 12, 2008 at 5:32 PM, Alan Dodd <[EMAIL PROTECTED]> wrote:

You asked for the frame at 1ps.  The trajectory starts at 125ps, so 
unsurprisingly the program does not give you an output.


- Original Message 
From: Liu Shiyong <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users 
Sent: Wednesday, March 12, 2008 10:07:17 PM
Subject: [gmx-users] trjconv output at a specified time

Hi, 

I want to output a structure in a given time, for example , in step 1 during 
minimization.

I tried the following command using dump:
trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb  -s 
r-l_1_oplsaa.input.tpr  -t0 0 -dump 1 

But It didnot work.

Output msg:

Select a group: 2
Selected 2: 'Protein-H'
trn version: GMX_trn_file (single precision)
Reading frame   0 time  125.000
Back Off! I just backed up m.pdb to ./#m.pdb.1#
Last frame 19 time 2418.000

WARNING no output, trajectory ended at 2418


gcq#76: "Baseball Heroes Only" (P.J. Harvey)

Best

-- 
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962 


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www interface or send it to [EMAIL PROTECTED]
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___
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-- 
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962


-Inline Attachment Follows-

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www interface or send it to [EMAIL PROTECTED]
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Tired of spam?  Yahoo! Mail has the best spam protection around 
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