[gmx-users] Gromacs-4 benchmarking

[vivek sharma]

Hi There,
I want to benchmark the scalability and speed for gromacs-4 on our cluster.
I want to know if there is any benchmarking activity already goin on? I have
browsed and got benchmarking for gromacs-3 and it seems that gromacs-4 is
much more scalable and faster than gromacs-3.
Can somebody suggest me with the standard dataset that can be used for
benchmarking?

thanks,
Vivek
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[gmx-users] water mediated hydrogen bond

[babu gokul]

Dear all
I have been looking for water mediated hydrogen bond in my simulation when i 
use 
g_hbond the -ins option it dose not showing the water mediated hydrogen bond 
could you please tell me how to get the hydrogen mediated hydrogen bond in 
gromacs ? is there any way to calculate hydrogen mediated hydrogen bond.

Thanking you
E R Azhagiya singam


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[gmx-users] water mediated hydrogen bond

[babu gokul]

Dear all
I have been looking for water mediated hydrogen bond in my simulation when i 
use 
g_hbond the -ins option it dose not showing the water mediated hydrogen bond 
could you please tell me how to get the hydrogen mediated hydrogen bond in 
gromacs ? is there any way to calculate hydrogen mediated hydrogen bond.

Thanking you
E R Azhagiya singam


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[gmx-users] Mix two solvents

[teklebrh]

Dear Gromacs,

I want to combine two separately equilibrated solvents into one mixed  
solvent file. How can I do that? I want to check the mixing effect of  
those solvents and try to check the density and volume change before  
and after mixing those solvents. I have equilibrated and run MD for  
2ns for each solvent and the density I got is pretty the same as of  
the experimental value. But now I want to combine both these files  
into one .gro file so that to see the volume/density change after MD  
and calculate the mixing effect. Can anybody help me on this issue?


Thank you

Rob

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Re: [gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon "Woodcrest"

[Mark Abraham]

- Original Message -
From: david.groc...@uk.fujitsu.com
Date: Tuesday, August 10, 2010 1:25
Subject: [gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon 
"Woodcrest"
To: gmx-users@gromacs.org

> Hi, this is the first time I have messaged this group, so please 
> bear with me.
> 
> I have had little trouble with previous versions (4.0.7 for 
> example), however with this version the pdb2gmx program gives a 
> segmentation fault error if run stand-alone, even with no input. 
> When compiled with debug, idb claims it is a "strlen" problem in 
> glibc. Running either grompp or mdrun or any other of the 
> executables without any input files merely yields the help 
> screen (as expected).
> 
> The single precision version works fine with Intel Compiler and 
> MKL !
> The double precision version works with GNU compiler and MKL, 
> but I need it to work with Intel

Not really. icc+MKL provides a miniscule improvement over gcc+FFTW3, so if the 
former gives trouble, use the latter. Search the archive, I probably published 
some 4.0.7 numbers.

> When compiling the double precision version 4.0.7, I found that 
> I needed to use the configure option --disable-x86-64-sse

That is probably to be expected. If these Woodcrest processors are in some 
Altix machine, then there's a history of unresolved problems with these 
nonbonded kernels on such machines. The problem seems not to be with the 
kernels. Search the archives if relevant.

> For 4.5b2, I have downloaded both the current version from Git 
> (05Aug - 1500 BST), as well as the tar.gz versions and got the 
> same problem.
> 
> I compiled with icc 10.1 and am using mkl 10.2 on very standard 
> Linux distribution.
> 
> Here is my configure line
> 
> ./configure CC=icc CPPFLAGS="-I$MKL_ROOT/include" LDFLAGS="-
> L$MKL_ROOT/lib/" --with-fft=mkl --prefix=$HOME/gromacs-
> 4.5b2/icc/double --enable-double --program-
> suffix=""LD=icc    

Something's gotten mangled here - the line's incomplete. One needs to take 
particular care to link correctly to MKL - consult the MKL docs for your system.

> Followed by "make -j 4 && make install"
> 
> Has anyone else tried this yet ? It seems like a quite trivial bug.

icc 11.1 + mkl + double works fine on my Intel Nehalem machine.

Mark
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Re: [gmx-users] A bug in gromacs tool 4.5

[Mark Abraham]

- Original Message -
From: Xiaohu Hu 
Date: Tuesday, August 10, 2010 10:26
Subject: [gmx-users] A bug in gromacs tool 4.5
To: gmx-users@gromacs.org

> Hi all,
> 
> I think the gromacs tools 4.5 may have a bug. So far I 
> experienced that several tools trjconv, g_rms, grmsf, g_covar, 
> g_anaeig crash with a segmentation fault if the trajectory read 
> in does not have the same atom number as the atom number in the 
> .tpr file. It seems to be a systematic problem. I can do the 
> same analysis without any problems with the older version of 
> gromacs tools, i. e. version 4.0.7.
> 
> Hope it could be fixed soon. Thanks!

Please submit a http://www.gromacs.org/Support/Bugzilla and attach files that 
demonstrate the problem. If a single trajectory frame will suffice, do that 
rather than upload a whole trajectory!

Mark

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[gmx-users] A bug in gromacs tool 4.5

[Xiaohu Hu]

Hi all,

I think the gromacs tools 4.5 may have a bug. So far I experienced that 
several tools trjconv, g_rms, grmsf, g_covar, g_anaeig crash with a 
segmentation fault if the trajectory read in does not have the same atom 
number as the atom number in the .tpr file. It seems to be a systematic 
problem. I can do the same analysis without any problems with the older 
version of gromacs tools, i. e. version 4.0.7.


Hope it could be fixed soon. Thanks!

Xiaohu
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[gmx-users] Conformational sampling

[chris . neale]

Nisha:

Simply applying available tools and seeing if the distribution looks  
okay is not a good plan. You should have a very well-defined idea of  
what you are trying to test and then pick a tool to get that done.


For example, perhaps you have a reference that provides the converged  
distribution of a dihedral and you want to see if your run reproduces  
this value. You would then use some tool, or combination of tools, to  
calculate the dihedral values and create a histogram of them.


Without an outside standard, it is certainly impossible to use a  
single run to prove that your sampling has converged. It is only  
possible to prove that it either (a) remains unconverged, or (b) that  
there is no evidence that it is unconverged.


In this case, if you really care about it, the best thing to do is to  
run a few separate simulations starting from different starting  
conformations (be sure to start from different dihedral basins). Then  
plot the time-average of some observables (e.g. the distribution of  
sampling of a given dihedral) and the values from different runs  
should "converge" to the same distribution if you run long enough --  
this is the true meaning of convergence, what many people do by way of  
things like block averaging is just a hack since one usually only has  
the resources to run a single trajectory.


And don't forget that there are more things to converge than just  
dihedrals. You could also look at pairwise combinations of dihedrals,  
etc. Note that I'm trying to keep the advice general here because I  
assume that you're eventually going to tackle something more complex  
than glycine.


Chris.

Well I guess, what I am trying to get at is, for my system I want to  
make sure that 100ns has covered all the conformational changes  
within the molecule, although I know there is not that much  
conformational changes for glycine molecule, but I just wanted to  
confirm. I did run g_angle command and I got the theta values for  
different groups and the distribution looks okay according to me (I  
compared the average angle values that I obtained from g_angle to  
the actual angle values.





Then that's probably the best you can do for a molecule as simple as  
glycine.  I

would certainly think that rotation about such few bonds would happen within
even less time than 100 ns.

-Justin




Quoting "Justin A. Lemkul" :




nishap.patel at utoronto.ca wrote:
So is there a way I can test for convergence for my zwitterion for  
 100ns run?




I'm not yet clear what you're assessing or how you define convergence.
In addition to what Chris said, you can look at dihedral transitions
with g_angle.  Surely there are a few dihedrals aside from standard
phi/psi, but I don't know what that's going to tell you.

-Justin



Quoting "Justin A. Lemkul" :




nishap.patel at utoronto.ca wrote:
Okay so I tried to analyze the torsion using g_chi and g_rama  
for   one glycine zwitterion in water. for g_rama I didn't see   
anything  in xmgrace, and same for g_chi. I used this command  
for  g_chi


g_chi -f traj.xtc -s gly.gro -phi -psi

When I run the command it says 1 residue with dihedrals found ,  
2   dihedrals found. But when I open the log file its empty and  
so  are  the histo-phi/psiGLY.xvg plots. I tried using g_dih but  
it  says:


Found 0 phi-psi combinations



For a zwitterion, these torsions don't exist.  To measure phi, you need
at least C-N-CA-N, and for psi N-CA-C-N.  For a single zwitterion, you
have only N-CA-C.  You need at least a dipeptide.

-Justin

I am not sure how to check for all torsion convergence for my
glycine zwitterion molecule. Am I missing something in the   
command  line?


-Nisha P

Quoting chris.neale at utoronto.ca:


Nisha,

The approach is dictated by the goal. What do you want from this? and
why are you doing it? e.g. if you want to test the FF, then it is a
good idea to at least include US as a part of your strategy; if you
want to determine if 100 ns of equilibrium sampling is sufficient to
converge all torsions, then obviously you should not be doing US. In
any event, would start by running some equilbrium simulations and
analyzing the torsions with g_rama, g_chi, g_dih, etc. Be sure to read
through the -h output of each program as there are some nuances.

Chris.

-- original message --

Hello,

I would like to do conformational sampling for my simulation of
one glycine in its zwitterionic form in water and obtain a PMF curve
to see if the system is equilibrated and that all possible torsions
are covered for my 100ns run. I am not sure how to approach this
issue. Is there a tutorial I can follow? Do I need to do umbrella
sampling and use WHAM to extract PMF?

I would appreciate some help!

Thanks.
Nisha P.






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Re: [gmx-users] installation problem fftw3 gromacs 4.5.b2

[Alpay Temiz]

thank you!

On Mon, Aug 9, 2010 at 4:40 PM, Justin A. Lemkul  wrote:

>
>
> Alpay Temiz wrote:
>
> 
>
>
>  checking for fftw3.h... yes
>> checking for main in -lfftw3... no
>> configure: error: Cannot find fftw3 library
>> [temi...@abcc1 gromacs-4.5-beta2]$ echo $LDFFLAGS
>>
>
> The proper environment variable is LDFLAGS, not LDFFLAGS.
>
> -Justin
>
>
>  -L/users/n2000546794/temizna/software/fftw/lib
>> [temi...@abcc1 gromacs-4.5-beta2]$ echo $CPPFLAGS
>> -I/users/n2000546794/temizna/software/fftw/include
>>
>>
>>
>>
> --
> 
>
> 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
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>
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Re: [gmx-users] Conformational sampling

[Justin A. Lemkul]

nishap.pa...@utoronto.ca wrote:
Well I guess, what I am trying to get at is, for my system I want to 
make sure that 100ns has covered all the conformational changes within 
the molecule, although I know there is not that much conformational 
changes for glycine molecule, but I just wanted to confirm. I did run 
g_angle command and I got the theta values for different groups and the 
distribution looks okay according to me (I compared the average angle 
values that I obtained from g_angle to the actual angle values.





Then that's probably the best you can do for a molecule as simple as glycine.  I 
would certainly think that rotation about such few bonds would happen within 
even less time than 100 ns.


-Justin




Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:
So is there a way I can test for convergence for my zwitterion for  
100ns run?




I'm not yet clear what you're assessing or how you define convergence.
In addition to what Chris said, you can look at dihedral transitions
with g_angle.  Surely there are a few dihedrals aside from standard
phi/psi, but I don't know what that's going to tell you.

-Justin



Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:
Okay so I tried to analyze the torsion using g_chi and g_rama for   
one glycine zwitterion in water. for g_rama I didn't see  anything  
in xmgrace, and same for g_chi. I used this command for  g_chi


g_chi -f traj.xtc -s gly.gro -phi -psi

When I run the command it says 1 residue with dihedrals found , 2   
dihedrals found. But when I open the log file its empty and so  
are  the histo-phi/psiGLY.xvg plots. I tried using g_dih but it  says:


Found 0 phi-psi combinations



For a zwitterion, these torsions don't exist.  To measure phi, you need
at least C-N-CA-N, and for psi N-CA-C-N.  For a single zwitterion, you
have only N-CA-C.  You need at least a dipeptide.

-Justin

I am not sure how to check for all torsion convergence for my   
glycine zwitterion molecule. Am I missing something in the  
command  line?


-Nisha P

Quoting chris.ne...@utoronto.ca:


Nisha,

The approach is dictated by the goal. What do you want from this? and
why are you doing it? e.g. if you want to test the FF, then it is a
good idea to at least include US as a part of your strategy; if you
want to determine if 100 ns of equilibrium sampling is sufficient to
converge all torsions, then obviously you should not be doing US. In
any event, would start by running some equilbrium simulations and
analyzing the torsions with g_rama, g_chi, g_dih, etc. Be sure to 
read

through the -h output of each program as there are some nuances.

Chris.

-- original message --

Hello,

I would like to do conformational sampling for my simulation of
one glycine in its zwitterionic form in water and obtain a PMF curve
to see if the system is equilibrated and that all possible torsions
are covered for my 100ns run. I am not sure how to approach this
issue. Is there a tutorial I can follow? Do I need to do umbrella
sampling and use WHAM to extract PMF?

I would appreciate some help!

Thanks.
Nisha P.



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--


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


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--


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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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Bioc

Re: [gmx-users] Conformational sampling

[nishap . patel]

Well I guess, what I am trying to get at is, for my system I want to  
make sure that 100ns has covered all the conformational changes within  
the molecule, although I know there is not that much conformational  
changes for glycine molecule, but I just wanted to confirm. I did run  
g_angle command and I got the theta values for different groups and  
the distribution looks okay according to me (I compared the average  
angle values that I obtained from g_angle to the actual angle values.





Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:
So is there a way I can test for convergence for my zwitterion for   
100ns run?




I'm not yet clear what you're assessing or how you define convergence.
In addition to what Chris said, you can look at dihedral transitions
with g_angle.  Surely there are a few dihedrals aside from standard
phi/psi, but I don't know what that's going to tell you.

-Justin



Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:
Okay so I tried to analyze the torsion using g_chi and g_rama for  
  one glycine zwitterion in water. for g_rama I didn't see   
anything  in xmgrace, and same for g_chi. I used this command for  
 g_chi


g_chi -f traj.xtc -s gly.gro -phi -psi

When I run the command it says 1 residue with dihedrals found , 2  
  dihedrals found. But when I open the log file its empty and so   
are  the histo-phi/psiGLY.xvg plots. I tried using g_dih but it   
says:


Found 0 phi-psi combinations



For a zwitterion, these torsions don't exist.  To measure phi, you need
at least C-N-CA-N, and for psi N-CA-C-N.  For a single zwitterion, you
have only N-CA-C.  You need at least a dipeptide.

-Justin

I am not sure how to check for all torsion convergence for my
glycine zwitterion molecule. Am I missing something in the   
command  line?


-Nisha P

Quoting chris.ne...@utoronto.ca:


Nisha,

The approach is dictated by the goal. What do you want from this? and
why are you doing it? e.g. if you want to test the FF, then it is a
good idea to at least include US as a part of your strategy; if you
want to determine if 100 ns of equilibrium sampling is sufficient to
converge all torsions, then obviously you should not be doing US. In
any event, would start by running some equilbrium simulations and
analyzing the torsions with g_rama, g_chi, g_dih, etc. Be sure to read
through the -h output of each program as there are some nuances.

Chris.

-- original message --

Hello,

I would like to do conformational sampling for my simulation of
one glycine in its zwitterionic form in water and obtain a PMF curve
to see if the system is equilibrated and that all possible torsions
are covered for my 100ns run. I am not sure how to approach this
issue. Is there a tutorial I can follow? Do I need to do umbrella
sampling and use WHAM to extract PMF?

I would appreciate some help!

Thanks.
Nisha P.



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--


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


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--


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] Conformational sampling

[Justin A. Lemkul]

nishap.pa...@utoronto.ca wrote:
So is there a way I can test for convergence for my zwitterion for 100ns 
run?




I'm not yet clear what you're assessing or how you define convergence.  In 
addition to what Chris said, you can look at dihedral transitions with g_angle. 
 Surely there are a few dihedrals aside from standard phi/psi, but I don't know 
what that's going to tell you.


-Justin



Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:
Okay so I tried to analyze the torsion using g_chi and g_rama for  
one glycine zwitterion in water. for g_rama I didn't see anything  in 
xmgrace, and same for g_chi. I used this command for g_chi


g_chi -f traj.xtc -s gly.gro -phi -psi

When I run the command it says 1 residue with dihedrals found , 2  
dihedrals found. But when I open the log file its empty and so are  
the histo-phi/psiGLY.xvg plots. I tried using g_dih but it says:


Found 0 phi-psi combinations



For a zwitterion, these torsions don't exist.  To measure phi, you need
at least C-N-CA-N, and for psi N-CA-C-N.  For a single zwitterion, you
have only N-CA-C.  You need at least a dipeptide.

-Justin

I am not sure how to check for all torsion convergence for my  
glycine zwitterion molecule. Am I missing something in the command  
line?


-Nisha P

Quoting chris.ne...@utoronto.ca:


Nisha,

The approach is dictated by the goal. What do you want from this? and
why are you doing it? e.g. if you want to test the FF, then it is a
good idea to at least include US as a part of your strategy; if you
want to determine if 100 ns of equilibrium sampling is sufficient to
converge all torsions, then obviously you should not be doing US. In
any event, would start by running some equilbrium simulations and
analyzing the torsions with g_rama, g_chi, g_dih, etc. Be sure to read
through the -h output of each program as there are some nuances.

Chris.

-- original message --

Hello,

 I would like to do conformational sampling for my simulation of
one glycine in its zwitterionic form in water and obtain a PMF curve
to see if the system is equilibrated and that all possible torsions
are covered for my 100ns run. I am not sure how to approach this
issue. Is there a tutorial I can follow? Do I need to do umbrella
sampling and use WHAM to extract PMF?

I would appreciate some help!

Thanks.
Nisha P.



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--


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


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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] Conformational sampling

[nishap . patel]

So is there a way I can test for convergence for my zwitterion for 100ns run?


Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:
Okay so I tried to analyze the torsion using g_chi and g_rama for   
one glycine zwitterion in water. for g_rama I didn't see anything   
in xmgrace, and same for g_chi. I used this command for g_chi


g_chi -f traj.xtc -s gly.gro -phi -psi

When I run the command it says 1 residue with dihedrals found , 2   
dihedrals found. But when I open the log file its empty and so are   
the histo-phi/psiGLY.xvg plots. I tried using g_dih but it says:


Found 0 phi-psi combinations



For a zwitterion, these torsions don't exist.  To measure phi, you need
at least C-N-CA-N, and for psi N-CA-C-N.  For a single zwitterion, you
have only N-CA-C.  You need at least a dipeptide.

-Justin

I am not sure how to check for all torsion convergence for my   
glycine zwitterion molecule. Am I missing something in the command   
line?


-Nisha P

Quoting chris.ne...@utoronto.ca:


Nisha,

The approach is dictated by the goal. What do you want from this? and
why are you doing it? e.g. if you want to test the FF, then it is a
good idea to at least include US as a part of your strategy; if you
want to determine if 100 ns of equilibrium sampling is sufficient to
converge all torsions, then obviously you should not be doing US. In
any event, would start by running some equilbrium simulations and
analyzing the torsions with g_rama, g_chi, g_dih, etc. Be sure to read
through the -h output of each program as there are some nuances.

Chris.

-- original message --

Hello,

 I would like to do conformational sampling for my simulation of
one glycine in its zwitterionic form in water and obtain a PMF curve
to see if the system is equilibrated and that all possible torsions
are covered for my 100ns run. I am not sure how to approach this
issue. Is there a tutorial I can follow? Do I need to do umbrella
sampling and use WHAM to extract PMF?

I would appreciate some help!

Thanks.
Nisha P.



--
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--


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


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Re: [gmx-users] Conformational sampling

[Justin A. Lemkul]

nishap.pa...@utoronto.ca wrote:
Okay so I tried to analyze the torsion using g_chi and g_rama for one 
glycine zwitterion in water. for g_rama I didn't see anything in 
xmgrace, and same for g_chi. I used this command for g_chi


g_chi -f traj.xtc -s gly.gro -phi -psi

When I run the command it says 1 residue with dihedrals found , 2 
dihedrals found. But when I open the log file its empty and so are the 
histo-phi/psiGLY.xvg plots. I tried using g_dih but it says:


Found 0 phi-psi combinations



For a zwitterion, these torsions don't exist.  To measure phi, you need at least 
C-N-CA-N, and for psi N-CA-C-N.  For a single zwitterion, you have only N-CA-C. 
 You need at least a dipeptide.


-Justin

I am not sure how to check for all torsion convergence for my glycine 
zwitterion molecule. Am I missing something in the command line?


-Nisha P

Quoting chris.ne...@utoronto.ca:


Nisha,

The approach is dictated by the goal. What do you want from this? and
why are you doing it? e.g. if you want to test the FF, then it is a
good idea to at least include US as a part of your strategy; if you
want to determine if 100 ns of equilibrium sampling is sufficient to
converge all torsions, then obviously you should not be doing US. In
any event, would start by running some equilbrium simulations and
analyzing the torsions with g_rama, g_chi, g_dih, etc. Be sure to read
through the -h output of each program as there are some nuances.

Chris.

-- original message --

Hello,

  I would like to do conformational sampling for my simulation of
one glycine in its zwitterionic form in water and obtain a PMF curve
to see if the system is equilibrated and that all possible torsions
are covered for my 100ns run. I am not sure how to approach this
issue. Is there a tutorial I can follow? Do I need to do umbrella
sampling and use WHAM to extract PMF?

I would appreciate some help!

Thanks.
Nisha P.



--
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Please search the archive at http://www.gromacs.org/search before 
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--


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


--
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Re: [gmx-users] Conformational sampling

[nishap . patel]

Okay so I tried to analyze the torsion using g_chi and g_rama for one  
glycine zwitterion in water. for g_rama I didn't see anything in  
xmgrace, and same for g_chi. I used this command for g_chi


g_chi -f traj.xtc -s gly.gro -phi -psi

When I run the command it says 1 residue with dihedrals found , 2  
dihedrals found. But when I open the log file its empty and so are the  
histo-phi/psiGLY.xvg plots. I tried using g_dih but it says:


Found 0 phi-psi combinations

I am not sure how to check for all torsion convergence for my glycine  
zwitterion molecule. Am I missing something in the command line?


-Nisha P

Quoting chris.ne...@utoronto.ca:


Nisha,

The approach is dictated by the goal. What do you want from this? and
why are you doing it? e.g. if you want to test the FF, then it is a
good idea to at least include US as a part of your strategy; if you
want to determine if 100 ns of equilibrium sampling is sufficient to
converge all torsions, then obviously you should not be doing US. In
any event, would start by running some equilbrium simulations and
analyzing the torsions with g_rama, g_chi, g_dih, etc. Be sure to read
through the -h output of each program as there are some nuances.

Chris.

-- original message --

Hello,

  I would like to do conformational sampling for my simulation of
one glycine in its zwitterionic form in water and obtain a PMF curve
to see if the system is equilibrated and that all possible torsions
are covered for my 100ns run. I am not sure how to approach this
issue. Is there a tutorial I can follow? Do I need to do umbrella
sampling and use WHAM to extract PMF?

I would appreciate some help!

Thanks.
Nisha P.



--
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Re: [gmx-users] installation problem fftw3 gromacs 4.5.b2

[Justin A. Lemkul]

Alpay Temiz wrote:




checking for fftw3.h... yes
checking for main in -lfftw3... no
configure: error: Cannot find fftw3 library
[temi...@abcc1 gromacs-4.5-beta2]$ echo $LDFFLAGS


The proper environment variable is LDFLAGS, not LDFFLAGS.

-Justin


-L/users/n2000546794/temizna/software/fftw/lib
[temi...@abcc1 gromacs-4.5-beta2]$ echo $CPPFLAGS
-I/users/n2000546794/temizna/software/fftw/include





--


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] installation problem fftw3 gromacs 4.5.b2

[Alpay Temiz]

Hi all

I am trying to install the latest version. I have installed fftw3 with
-enable float and enable thread options, but I am still getting a fftw3
error.
the fftw/lib location has all these files:
 libfftw3f.a  libfftw3f_threads.la*  libfftw3_threads.la*
../ libfftw3f.la*libfftw3.la*   pkgconfig/
libfftw3.a  libfftw3f_threads.a  libfftw3_threads.a

my config command is below:

[temi...@abcc1 gromacs-4.5-beta2]$  ./configure
--prefix=/users/n2000546794/temizna/gromacs.4.5.b2 --program-prefix=452
--enable-double  --enable-mpi  --with-x


checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for cc... cc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of cc... gcc3
checking dependency style of cc... gcc3
checking for mpxlc... no
checking for mpicc... mpicc
checking whether the MPI cc command works... yes
checking for MPI_IN_PLACE in collective operations... yes
checking for catamount... no
checking how to run the C preprocessor... mpicc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether ln -s works... yes
checking whether mpicc accepts -O3... yes
checking whether mpicc accepts -msse2... yes
checking whether mpicc accepts -funroll-all-loops... yes
checking whether mpicc accepts -std=gnu99... yes
checking whether mpicc accepts -fexcess-precision=fast... no
checking whether mpicc accepts  -O3 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes
checking whether byte ordering is bigendian... no
checking that size_t can hold pointers... yes
checking for SIGUSR1... yes
checking for pipes... yes
checking floating-point format... IEEE754 (little-endian byte and word
order)
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /bin/sed
checking for ld used by mpicc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... yes
checking whether mpicc accepts -g... yes
checking dependency style of mpicc... gcc3
checking how to run the C++ preprocessor... mpicc -E
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from mpicc object... failed
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if mpicc supports -fno-rtti -fno-exceptions... no
checking for mpicc option to produce PIC... -fPIC
checking if mpicc PIC flag -fPIC works... yes
checking if mpicc static flag -static works... yes
checking if mpicc supports -c -o file.o... yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by mpicc... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking for mpicc option to produce PIC... -fPIC
checking if mpicc PIC flag -fPIC works... yes
checking if mpicc static flag -static works... no
checking if mpicc supports -c -o file.o... yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for 

Re: [gmx-users] abnormal stop of job

[Elton Carvalho]

In tis case it must have been your sysadmin or your queueing system.
Check the other answers in this thread.

On Thu, Aug 5, 2010 at 10:30 PM, Samrat Pal  wrote:
> Hi Elton,
> But I have neither killed the job nor I pressed Ctrl-C in the foreground.
> The job was practically running background.
> Thanks
> Atanu
>
>
> 
> From: Elton Carvalho 
> To: Discussion list for GROMACS users 
> Sent: Thu, August 5, 2010 1:59:39 PM
> Subject: Re: [gmx-users] abnormal stop of job
>
> On Thu, Aug 5, 2010 at 1:37 PM, Samrat Pal  wrote:
>>
>> Received the TERM signal, stopping at the next step
>
> The TERM signal is the default signal sent by the command "kill" to
> stop a job. Pressing Ctrl-C while the program is running on the
> foreground has the same effect.
>
> --
> 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
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
> --
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>



-- 
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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[gmx-users] Re: cutoff for implicit solvent in gromacs4.5

[BIN ZHANG]

Dear Per:
Thanks for your reply.
I did start the simulation from an equilibrated structure. Instead of  
setting them to 0, if I simply use a large cut-off (say 1.6),  
everything works just fine.

Best,
Bin




Hi,

for implicit solvent, people generally use longer cut-offs, as you  
noted.


There can be many reasons for your seg. fault, however.
Did you do energy minimization before starting md?
Please also test the same system with using a cut-off to see if that  
works.


/Per



8 aug 2010 kl. 22.36 skrev BIN ZHANG:

> But the problem is with this set up, I will always get a  
"Segmentation fault" with gromacs VERSION 4.5-beta2.

>
> Is this supposed to be a bug or for this version, I can only use a  
large cutoff?


On Aug 8, 2010, at 10:56 PM, gmx-users-requ...@gromacs.org wrote:


Send gmx-users mailing list submissions to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."
Today's Topics:

  1. Best forcefield for DMPC - Protein system (Deniz KARASU)
  2. Best forcefield for DMPC - Protein system (Deniz KARASU)
  3. cutoff for implicit solvent in gromacs4.5 (BIN ZHANG)
  4. Large output files and limited disk space. How do Ihandle
 them? (NG HUI WEN)
  5. Re: Large output files and limited disk space. How do I
 handle them? (Mark Abraham)

From: Deniz KARASU 
Date: August 8, 2010 8:45:08 AM PDT
To: gmx-users@gromacs.org
Subject: [gmx-users] Best forcefield for DMPC - Protein system
Reply-To: Discussion list for GROMACS users 


Hi,

I am planing to use 53a6 ff for my membrane protein system. And I can
use Kukol 2009 lipid or Roger 2010 lipid and topology  so I wonder  
is there any

problem about 53a6 force field and what is the most suitable force
field for membrane protein systems?

I read from http://www.mail-archive.com/gmx-users@gromacs.org/msg27700.html
mail that there are some problems about 53a6 forcefield.


1) Kukol, A., 2009. Lipid models for united-atom molecular dynamics
simulations of proteins
2) D Poger, WF Van Gunsteren,  2010.  A new force field for simulating
phosphatidylcholine bilayers.

Thanks.
Deniz.




From: Deniz KARASU 
Date: August 8, 2010 8:47:48 AM PDT
To: gmx-users@gromacs.org
Subject: [gmx-users] Best forcefield for DMPC - Protein system
Reply-To: Discussion list for GROMACS users 


Hi,

I am planing to use 53a6 ff for my membrane protein system. And I can
use Kukol 2009 lipid or Roger 2010 lipid and topology  so I wonder  
is there any

problem about 53a6 force field and what is the most suitable force
field for membrane protein systems?

I read from http://www.mail-archive.com/gmx-users@gromacs.org/msg27700.html
mail that there are some problems about 53a6 forcefield.


1) Kukol, A., 2009. Lipid models for united-atom molecular dynamics
simulations of proteins
2) D Poger, WF Van Gunsteren,  2010.  A new force field for simulating
phosphatidylcholine bilayers.

Thanks.
Deniz.




From: BIN ZHANG 
Date: August 8, 2010 1:36:39 PM PDT
To: Discussion list for GROMACS users 
Subject: [gmx-users] cutoff for implicit solvent in gromacs4.5
Reply-To: Discussion list for GROMACS users 


Dear all:

I have a question about the appropriate cut-off usage in implicit  
solvent simulation. After googling for a while, I found most  
references mentioning using non cut-off for these type of  
simulations. For non cut-off,  I assume in gromacs using the  
following parameters:


coulombtype  = Cut-off
vdwtype = Cut-off
nstype   = grid
nstlist= 0
rlist= 0
rcoulomb  = 0
rvdw = 0

; implicit solvent options
implicit_solvent =   GBSA
gb_epsilon_solvent   =   80
gb_algorithm =   OBC
rgbradii  = 0   ; need to be equal to rlist

But the problem is with this set up, I will always get a  
"Segmentation fault" with gromacs VERSION 4.5-beta2.


Is this supposed to be a bug or for this version, I can only use a  
large cutoff?


Thanks,
Bin





From: "NG HUI WEN" 
Date: August 8, 2010 8:04:57 PM PDT
To: 
Subject: [gmx-users] Large output files and limited disk space. How  
do I handle them?

Reply-To: Discussion list for GROMACS users 


Dear gmxusers,

I have a very basic question here which I hope someone could help me  
with. I was running a couple of simulations over the weekend on a  
shared cluster and both came to a stop for the same reasons:


Program mdrun_mpi, VERSION 4.0.7
Source code file: trnio.c, line: 252
File input/output error:
Cannot write trajectory frame; maybe you are out of quota?

Inde

[gmx-users] Conformational sampling

[chris . neale]

Nisha,

The approach is dictated by the goal. What do you want from this? and  
why are you doing it? e.g. if you want to test the FF, then it is a  
good idea to at least include US as a part of your strategy; if you  
want to determine if 100 ns of equilibrium sampling is sufficient to  
converge all torsions, then obviously you should not be doing US. In  
any event, would start by running some equilbrium simulations and  
analyzing the torsions with g_rama, g_chi, g_dih, etc. Be sure to read  
through the -h output of each program as there are some nuances.


Chris.

-- original message --

Hello,

 I would like to do conformational sampling for my simulation of
one glycine in its zwitterionic form in water and obtain a PMF curve
to see if the system is equilibrated and that all possible torsions
are covered for my 100ns run. I am not sure how to approach this
issue. Is there a tutorial I can follow? Do I need to do umbrella
sampling and use WHAM to extract PMF?

I would appreciate some help!

Thanks.
Nisha P.



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Re: [gmx-users] abnormal stop of job

[ms]

On 05/08/10 17:37, Samrat Pal wrote:

Hi all,
   I have been running a simulation of 200 ns length and it suddenly
stoped at 67 ns showing the following line -

Received the TERM signal, stopping at the next step

I have checked the time steps properly and there is no error. What should I do
now? Please suggest.


If it received a TERM signal it seems to indicate someone or something 
else has killed your process.

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Re: [gmx-users] Fatal Error - RMSD Calculation

[Justin A. Lemkul]

deisy yurley rodriguez sarmiento wrote:

Hi everyone,

I want to calculate the RMSD, and a few minutes to start the 
calculation, appears that Fatal Error:

calloc for bond_mat[i] (nelem=50001, elsize=4, file gmx_rms.c, line 650)

I don't have any idea what is the problem.


Sounds like a memory allocation problem.

http://www.gromacs.org/Documentation/Errors#Cannot_allocate_memory

If you want advice for troubleshooting, provide your command line, groups chosen 
for analysis, description of the system, etc.


-Justin



Thanks in advance!!!...

Deisy Y. Rodriguez S.
Practicante de Computos Avanzados
Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX
Tel. 6344000  ext. 2792
Universidad Industrial de Santander




--


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] Another test

[David van der Spoel]

This time from gmail.

David.
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[gmx-users] abnormal stop of job

[chris . neale]

Sounds like you killed the job, or your sysadmin killed it, or it  
timed out if you are on a cluster with a walltime limit.


-- original message --

Hi all,
  I have been running a simulation of 200 ns length and it suddenly
stoped at 67 ns showing the following line -

Received the TERM signal, stopping at the next step

I have checked the time steps properly and there is no error. What should I do
now? Please suggest.

Thanks
Samrat


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Re: [gmx-users] cutoff for implicit solvent in gromacs4.5

[Per Larsson]

Hi,

for implicit solvent, people generally use longer cut-offs, as you noted.

There can be many reasons for your seg. fault, however.
Did you do energy minimization before starting md? 
Please also test the same system with using a cut-off to see if that works.

/Per



8 aug 2010 kl. 22.36 skrev BIN ZHANG:

> But the problem is with this set up, I will always get a "Segmentation fault" 
> with gromacs VERSION 4.5-beta2.
> 
> Is this supposed to be a bug or for this version, I can only use a large 
> cutoff?

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RE: [gmx-users] hyperthreading

[Berk Hess]

Hi,

In Gromacs 4.5 there is no difference, since it does not use real thread 
parallelization.
Gromacs 4.5 has a built-in threaded MPI library, but openmpi also has an 
efficient
MPI implementation for shared memory machines. But even with proper thread
parallelization I expect the same 15 to 20% performance improvement.
(I guess the lower 8% number is because of loss when going from 8 to 16 
processes
for mdrun for that particular system)

Berk

> Date: Mon, 9 Aug 2010 11:36:35 -0400
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] hyperthreading
> 
> I haven't tried mdrun -nt based hyperthreading, but I have tested  
> using -np 16 on an 8 core box. I get an 8% to 18% performance increase  
> when using -np 16 and optimizing -npme as compared to -np 8 and  
> optimizing -npme. This is on a cluster of Intel Xeon E5540 aka  
> "Nehalem" with 2 quad cores in a single box and using gromacs 4.0.7. I  
> now regularly overload the number of processes.
> 
> selected examples:
> System A with 250,000 atoms:
> mdrun -np 8  -npme -11.15 ns/day
> mdrun -np 8  -npme  21.02 ns/day
> mdrun -np 16 -npme  20.99 ns/day
> mdrun -np 16 -npme  41.36 ns/day <-- 118 % performance vs 1.15 ns/day
> mdrun -np 15 -npme  31.32 ns/day
> 
> System B with 35,000 atoms (4 fs timestep):
> mdrun -np 8  -npme -122.66 ns/day
> mdrun -np 8  -npme  223.06 ns/day
> mdrun -np 16 -npme -122.69 ns/day
> mdrun -np 16 -npme  424.90 ns/day <-- 108 % performance vs 23.06 ns/day
> mdrun -np 56 -npme 1614.15 ns/day
> 
> Cutoffs and timesteps differ between these runs, but both use PME and  
> explicit water.
> 
> I'd be interested in hearing about any comparisons between -np based  
> process overloading and -nt based hyperthreading.
> 
> Hope it helps,
> Chris.
> 
> -- original message --
> 
> Hi,
> 
> These are nehalem Xeons I presume?
> Then you get 15 to 20% more performance in Gromacs running 2 vs 1  
> thread or process per physical core.
> 
> Berk
> 
> > Date: Fri, 6 Aug 2010 09:24:11 -0500
> > From: dmobley at gmail.com
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] hyperthreading
> >
> > Dear All,
> >
> > I'm putting together a new Dell Xeon cluster running ROCKS 5.3 which
> > uses CENTOS (6 I believe). This is currently ~20 dual quad-cores with
> > roughly 16 GB of RAM each.
> >
> > In any case, I wanted to inquire about hyperthreading. Does anyone
> > have experience on similar machines with vs. without hyperthreading?
> > The ROCKS users list suggests that hyperthreading ought always be off
> > for HPC applications, which sounds overly simplistic to me, though I
> > more or less follow the logic of this.
> >
> > So, has anyone done any benchmarking yet in a similar setting, and
> > what thoughts do you have? I obviously can do some benchmarking myself
> > as well but I thought I'd check in with the list first.
> >
> > Thanks so much,
> > David
> >
> >
> > -- 
> > David Mobley
> > dmobley at gmail.com
> > 504-383-3662
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] abnormal stop of job

[Szilárd Páll]

Hi,

The message is quite obvious about what happened: mdrun received a
TERM signal and therefor it stopped (see: man 7 signal or
http://linux.die.net/man/7/signal).

Figuring out the reason who and why sent a TERM signal to your mdrun
will be your task, but I can think of 2 basic scenarios: (I) you (or
someone else) manually kill-ed your mdrun; (II) it ran out of the time
allocated for this process (on a cluster?).

Cheers,
--
Szilárd


On Thu, Aug 5, 2010 at 6:37 PM, Samrat Pal  wrote:
> Hi all,
>   I have been running a simulation of 200 ns length and it suddenly
> stoped at 67 ns showing the following line -
>
> Received the TERM signal, stopping at the next step
>
> I have checked the time steps properly and there is no error. What should I
> do now? Please suggest.
>
> Thanks
> Samrat
>
>
> --
> gmx-users mailing list    gmx-us...@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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>
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[gmx-users] hyperthreading

[chris . neale]

I haven't tried mdrun -nt based hyperthreading, but I have tested  
using -np 16 on an 8 core box. I get an 8% to 18% performance increase  
when using -np 16 and optimizing -npme as compared to -np 8 and  
optimizing -npme. This is on a cluster of Intel Xeon E5540 aka  
"Nehalem" with 2 quad cores in a single box and using gromacs 4.0.7. I  
now regularly overload the number of processes.


selected examples:
System A with 250,000 atoms:
mdrun -np 8  -npme -11.15 ns/day
mdrun -np 8  -npme  21.02 ns/day
mdrun -np 16 -npme  20.99 ns/day
mdrun -np 16 -npme  41.36 ns/day <-- 118 % performance vs 1.15 ns/day
mdrun -np 15 -npme  31.32 ns/day

System B with 35,000 atoms (4 fs timestep):
mdrun -np 8  -npme -122.66 ns/day
mdrun -np 8  -npme  223.06 ns/day
mdrun -np 16 -npme -122.69 ns/day
mdrun -np 16 -npme  424.90 ns/day <-- 108 % performance vs 23.06 ns/day
mdrun -np 56 -npme 1614.15 ns/day

Cutoffs and timesteps differ between these runs, but both use PME and  
explicit water.


I'd be interested in hearing about any comparisons between -np based  
process overloading and -nt based hyperthreading.


Hope it helps,
Chris.

-- original message --

Hi,

These are nehalem Xeons I presume?
Then you get 15 to 20% more performance in Gromacs running 2 vs 1  
thread or process per physical core.


Berk


Date: Fri, 6 Aug 2010 09:24:11 -0500
From: dmobley at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] hyperthreading

Dear All,

I'm putting together a new Dell Xeon cluster running ROCKS 5.3 which
uses CENTOS (6 I believe). This is currently ~20 dual quad-cores with
roughly 16 GB of RAM each.

In any case, I wanted to inquire about hyperthreading. Does anyone
have experience on similar machines with vs. without hyperthreading?
The ROCKS users list suggests that hyperthreading ought always be off
for HPC applications, which sounds overly simplistic to me, though I
more or less follow the logic of this.

So, has anyone done any benchmarking yet in a similar setting, and
what thoughts do you have? I obviously can do some benchmarking myself
as well but I thought I'd check in with the list first.

Thanks so much,
David


--
David Mobley
dmobley at gmail.com
504-383-3662



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Re: [gmx-users] abnormal stop of job

[Justin A. Lemkul]

Samrat Pal wrote:

Hi all,
  I have been running a simulation of 200 ns length and it 
suddenly stoped at 67 ns showing the following line -
 
Received the TERM signal, stopping at the next step


I have checked the time steps properly and there is no error. What 
should I do now? Please suggest.




Restart from the last checkpoint.  Something in your system told mdrun to stop 
running.  If there's nothing in your .log file, then it's not Gromacs' fault 
that the job ended.  We usually get these when a node in the cluster bugs out or 
the interconnect fails for some reason.


-Justin


Thanks
Samrat



--


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] abnormal stop of job

[Samrat Pal]

Hi Elton,
But I have neither killed the job nor I pressed Ctrl-C in the foreground. The 
job was practically running background.
Thanks
Atanu






From: Elton Carvalho 
To: Discussion list for GROMACS users 
Sent: Thu, August 5, 2010 1:59:39 PM
Subject: Re: [gmx-users] abnormal stop of job

On Thu, Aug 5, 2010 at 1:37 PM, Samrat Pal  wrote:
>
> Received the TERM signal, stopping at the next step

The TERM signal is the default signal sent by the command "kill" to
stop a job. Pressing Ctrl-C while the program is running on the
foreground has the same effect.

-- 
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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[gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon "Woodcrest"

[David.Grocutt]

Hi, this is the first time I have messaged this group, so please bear with me.

I have had little trouble with previous versions (4.0.7 for example), however 
with this version the pdb2gmx program gives a segmentation fault error if run 
stand-alone, even with no input. When compiled with debug, idb claims it is a 
"strlen" problem in glibc. Running either grompp or mdrun or any other of the 
executables without any input files merely yields the help screen (as expected).

The single precision version works fine with Intel Compiler and MKL !
The double precision version works with GNU compiler and MKL, but I need it to 
work with Intel

When compiling the double precision version 4.0.7, I found that I needed to use 
the configure option --disable-x86-64-sse


For 4.5b2, I have downloaded both the current version from Git (05Aug - 1500 
BST), as well as the tar.gz versions and got the same problem.

I compiled with icc 10.1 and am using mkl 10.2 on very standard Linux 
distribution.

Here is my configure line

./configure CC=icc CPPFLAGS="-I$MKL_ROOT/include" LDFLAGS="-L$MKL_ROOT/lib/" 
--with-fft=mkl --prefix=$HOME/gromacs-4.5b2/icc/double --enable-double 
--program-suffix=""LD=icc

Followed by "make -j 4 && make install"

Has anyone else tried this yet ? It seems like a quite trivial bug.

Thanks

David

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[gmx-users] Fatal Error - RMSD Calculation

[deisy yurley rodriguez sarmiento]

Hi everyone,

I want to calculate the RMSD, and a few minutes to start the calculation, 
appears that Fatal Error:
calloc for bond_mat[i] (nelem=50001, elsize=4, file gmx_rms.c, line 650)

I don't have any idea what is the problem.

Thanks in advance!!!...

Deisy Y. Rodriguez S.
Practicante de Computos Avanzados
Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX
Tel. 6344000  ext. 2792
Universidad Industrial de Santander



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RE: [gmx-users] pdb file

[Dallas Warren]

This is a VMD issue, it estimates which atoms are bonded together by the
distance that the atoms are separated.  Obviously, the bonds that you
see "disappear" are due to them being separated by a distance larger
than what VMD would say is "bonded".

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of leila karami
> Sent: Friday, 6 August 2010 11:00 PM
> To: gmx-users
> Subject: [gmx-users] pdb file
> 
> Hi gromacs users
> 
> I obtained pdb input file for gromacs from STRAP program. this pdb
> file coantains protein and dna. this pdb file was obtaind form
> superposition of 2 other pdb files. there is one problem: when I see
> pdb file obtained from STRAP program by VMD, some bonds are
> disappeared whereas when I open same file by text editor all things
> are normal.as I can not attached this pdb file, I put residues 10-40
> corresponding to protein from pdb.
> 
> please guide me
> 
> 
> ATOM 95  N   GLY A  10  -1.818  -6.947 -14.722  1.00  0.00
> N
> ATOM 96  CA  GLY A  10  -1.256  -7.638 -13.576  1.00  0.00
> C
> ATOM 97  C   GLY A  10  -2.311  -8.357 -12.758  1.00  0.00
> C
> ATOM 98  O   GLY A  10  -3.368  -7.797 -12.468  1.00  0.00
> O
> ATOM 99  H   GLY A  10  -2.768  -7.530 -14.939  1.00  0.00
> H
> ATOM100  HA2 GLY A  10  -0.531  -8.359 -13.923  1.00  0.00
> H
> ATOM101  HA3 GLY A  10  -0.758  -6.916 -12.944  1.00  0.00
> H
> ATOM102  N   GLN A  11  -2.230  -9.602 -12.388  1.00  0.00
> N
> ATOM103  CA  GLN A  11  -2.957 -10.399 -11.600  1.00  0.00
> C
> ATOM104  C   GLN A  11  -2.588 -10.366 -10.121  1.00  0.00
> C
> ATOM105  O   GLN A  11  -1.978 -11.302  -9.604  1.00  0.00
> O
> ATOM106  CB  GLN A  11  -2.977 -11.843 -12.104  1.00  0.00
> C
> ATOM107  CG  GLN A  11  -3.963 -12.790 -13.236  1.00  0.00
> C
> ATOM108  CD  GLN A  11  -5.336 -11.508 -12.942  1.00  0.00
> C
> ATOM109  OE1 GLN A  11  -5.869 -11.673 -11.845  1.00  0.00
> O
> ATOM110  NE2 GLN A  11  -5.918 -10.829 -13.926  1.00  0.00
> N
> ATOM111  H   GLN A  11  -1.164  -9.991 -12.649  1.00  0.00
> H
> ATOM112  HA  GLN A  11  -3.941  -9.972 -11.722  1.00  0.00
> H
> ATOM113  HB2 GLN A  11  -1.990 -12.102 -12.454  1.00  0.00
> H
> ATOM114  HB3 GLN A  11  -3.242 -12.493 -11.282  1.00  0.00
> H
> ATOM115  HG2 GLN A  11  -3.582 -11.616 -14.132  1.00  0.00
> H
> ATOM116  HG3 GLN A  11  -4.590 -13.144 -13.395  1.00  0.00
> H
> ATOM117 HE21 GLN A  11  -5.434 -10.739 -14.774  1.00  0.00
> H
> ATOM118 HE22 GLN A  11  -6.805 -10.449 -13.763  1.00  0.00
> H
> ATOM119  N   VAL A  12  -2.960  -9.284  -9.446  1.00  0.00
> N
> ATOM120  CA  VAL A  12  -2.670  -9.130  -8.270  1.00  0.00
> C
> ATOM121  C   VAL A  12  -3.937  -8.829  -7.235  1.00  0.00
> C
> ATOM122  O   VAL A  12  -4.775  -8.340  -7.664  1.00  0.00
> O
> ATOM123  CB  VAL A  12  -1.644  -8.800  -7.782  1.00  0.00
> C
> ATOM124  CG1 VAL A  12  -1.342  -7.874  -6.296  1.00  0.00
> C
> ATOM125  CG2 VAL A  12  -0.370  -8.270  -8.571  1.00  0.00
> C
> ATOM126  H   VAL A  12  -3.444  -8.572  -9.914  1.00  0.00
> H
> ATOM127  HA  VAL A  12  -2.246 -10.600  -7.670  1.00  0.00
> H
> ATOM128  HB  VAL A  12  -2.710  -7.780  -8.126  1.00  0.00
> H
> ATOM129 HG11 VAL A  12  -2.268  -7.887  -5.739  1.00  0.00
> H
> ATOM130 HG12 VAL A  12  -0.718  -8.697  -5.980  1.00  0.00
> H
> ATOM131 HG13 VAL A  12  -0.828  -6.941  -6.117  1.00  0.00
> H
> ATOM132 HG21 VAL A  12   0.203  -9.430  -8.830  1.00  0.00
> H
> ATOM133 HG22 VAL A  12  -0.625  -8.588  -9.572  1.00  0.00
> H
> ATOM134 HG23 VAL A  12   0.215  -7.363  -8.621  1.00  0.00
> H
> ATOM135  N   ARG A  13  -4.710  -9.465  -6.760  1.00  0.00
> N
> ATOM136  CA  ARG A  13  -5.236  -9.265  -5.223  1.00  0.00
> C
> ATOM137  C   ARG A  13  -5.140  -9.881  -3.845  1.00  0.00
> C
> ATOM138  O   ARG A  13  -4.412 -10.947  -3.720  1.00  0.00
> O
> ATOM139  CB  ARG A  13  -6.480  -9.873  -5.874  1.00  0.00
> C
> ATOM140  CG  ARG A  13  -7.779  -9.475  -5.194  1.00  0.00
> C
> ATOM141  CD  ARG A  13  -8.147 -10.444  -4.830  1.00  0.00
> C
> ATOM142  NE  ARG A  13  -8.819 -11.635  -4.596  1.00  0.00
> N
> ATOM143  CZ  ARG A  13 -10.800 -11.611  -5.186  1.00  0.00
> C
> ATOM144  NH1 ARG A  13 -10.654 -10.463  -5.337  1.00  0.00
> N
> ATOM145  NH2 ARG A  13 -10.555 -1

[gmx-users] Reduced Units

[pojeda]

Hi,

I want to use the pme algorithm in GROMACS. Thge size of my box is
8.2x8.2x8.2 in reduced units. I am considering a collection of 1000
of CO2 molecules. If I am using reduced units, the values of the
parameters "rcoulomb=0.9" I think should be converted to reduced
units "rcoulomb=2.45" (my \sigma=0.366nm). But my question is how
can one convert the value of "fourierspacing=0.12" to reduced units?




(This script is in SI standard units)
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = pme
rcoulomb-switch  = 0
rcoulomb = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r= 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch  = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no


Thanks.

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Re: [gmx-users] double precision pdb2gmx - 4.5beta2 - segmentation fault - icc compiler (gcc is fine)

[Rossen Apostolov]

 This was already reported, there is a bugzilla filed already and we 
are looking at fixing it.


http://bugzilla.gromacs.org/show_bug.cgi?id=495

Rossen

On 8/6/10 2:45 PM, david.groc...@uk.fujitsu.com wrote:

Has anyone else tried this ?

The single precision version is fine with icc.

Thanks

David

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[gmx-users] double precision pdb2gmx - 4.5beta2 - segmentation fault - icc compiler (gcc is fine)

[David.Grocutt]

Has anyone else tried this ?

The single precision version is fine with icc.

Thanks

David

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 Hayes Park Central, Hayes End Road, Hayes, Middlesex, UB4 8FE
 Registered No. 4153469
 
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 may contain information which is privileged and confidential. Unauthorised
 use or copying for disclosure is strictly prohibited. The fact that this
 e-mail has been scanned by Trendmicro Interscan does not guarantee that 
 it has not been intercepted or amended nor that it is virus-free.

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[gmx-users] deneme

[Deniz KARASU]

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Re: [gmx-users] Lipid parameters for GROMOS96 force fields

[Deniz KARASU]

Hi,

I am planing to use 53a6 ff for my membrane protein system. And I can
use Kukol 2009 lipid or Roger 2010 lipids  so I wonder is there any
problem about 53a6 force field and what is the most suitable force
field for membrane protein systems?

1) Kukol, A., 2009. Lipid models for united-atom molecular dynamics
simulations of proteins
2) D Poger, WF Van Gunsteren,  2010.  A new force field for simulating
phosphatidylcholine bilayers.

Thanks.
Deniz.

On Fri, Jan 22, 2010 at 11:36 AM, XAvier Periole  wrote:
>
> Here is another paper related to the secondary structure propensity
> of different force field.
> Are current Molecular Dynamics FFs too helical? Best et al: BiophysJ-2008
> doi:10.1529/biophysj.108.132696
> Note that these papers do not report the unstability of helices in proteins!
> On Jan 22, 2010, at 1:03 AM, Krzysztof Mlynarczyk wrote:
>
> Thank you!!!
> The evidence presented in this paper is stunning. It also stresses the 
> importance of using the electrostatics treatment that was originally used for 
> development of a particular force field, e.g. reaction field in case of G96 - 
> the popular PME in connection with G53a6 results in even stronger beta sheet 
> bias. This way using this force field is out of the question, unless until 
> corrections are made and tested. I need a different solution for my problem.
>
> Christopher
>
> 2010/1/21 Erik Marklund 
>>
>> It is documented. Have a look at this one:
>>
>> Dirk Matthes and Bert L. de Groot.  Secondary structure propensities in 
>> peptide folding simulations: A systematic comparison of molecular mechanics 
>> interaction schemes.  Biophys. J.  97:599-608 (2009)
>>
>> Erik
>>
>> XAvier Periole skrev:
>>>
>>> The instability of helices with the G53a6 force field is definitely real
>>> and unfortunately not documented. Some people are working on it ...
>>>
>>> I would advise to be very carefull in interpreting results with this FF.
>>>
>>> XAvier.
>>>
>>> On Jan 21, 2010, at 2:13 PM, Justin A. Lemkul wrote:
>>>


 Krzysztof Mlynarczyk wrote:
>
> 2010/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>>
>   Krzysztof Mlynarczyk wrote:
>       2. If not, is there any way to derive the proper parameters for
>       the force field of my choice using the lipid parameters from
>       Peter Tieleman's website or e.g. the parameters published by
>       Andreas Kukol for G53a6?
>   I don't see why you need to do such reverse engineering.  The Kukol
>   parameters for lipids under 53a6 can be directly combined with a
>   G53a6 protein without any issues; I believe that was the purpose of
>   the whole new derivation :)
> I received a message that G53a6 is beta-sheet biased and alpha helices do 
> not perform as well as they should. My protein contains 7 transmembrane 
> helices, that's why I'm worried.

 Is this published somewhere?  That would be important information.  
 Perhaps this is the case for model peptides or short fragments, but I have 
 certainly done a number of simulations using 53a6 with well-folded 
 globular proteins and I do not see any such instability (i.e., alpha->beta 
 conversion or unwinding of alpha-helices).  I do believe it is possible in 
 certain scenarios, but I don't know that a large 7TM protein like yours 
 would suffer adversely.

> I know that there are changes between parameter sets both in non-bonded 
> and bonded terms and one rtp entry will probably not work well when 
> pasted into a different force field from the same family. G96 family uses 
> symbols like gd_5 that are substituted by appropriate parameters later 
> through the use of preprocessor. While it is possible to find that gd_5 
> is the same as gd_15 in another version of G96 and substitute those 
> symbols in topologies, the changes in non bonded parameters still can 
> spoil what was working well elsewhere. That's why I was also asking for 
> some checked and ready-to-use topologies for a particular force field.

 Many of the bonded parameters carry over between force fields, but 
 certainly new entries were created between 43a2 and 53a6, so yes, some 
 re-working would likely be necessary.  There is a lipid 43a2 parameter set 
 on the User Contribution site, like I said before, I just don't know if 
 there is a reference for it.

>   As an aside, you are quite right that multiple force fields within
>   the same simulation is incorrect.  However, the Berger lipid
>   parameters may be an exception to this rule, since they are really a
>   hybridized version of OPLS-UA and Gromos87 parameters (some of which
>   were modified anyway), so they really don't belong to any one
>   particular force field.  The Berger/G87 combination is widely used,
>   but essentially amounts to the following: lipid interactions are
>   Berger-Berger or OPLS-OPLS interactio

Re: [gmx-users] Large output files and limited disk space. How do I handle them?

[Justin A. Lemkul]

NG HUI WEN wrote:

Dear gmxusers,
 
I have a very basic question here which I hope someone could help me 
with. I was running a couple of simulations over the weekend on a shared 
cluster and both came to a stop for the same reasons:
 
Program mdrun_mpi, VERSION 4.0.7

Source code file: trnio.c, line: 252
File input/output error:
Cannot write trajectory frame; maybe you are out of quota?
 
Indeed there were quite a number of large files in my user 
directory (e.g. the .trr files and etc). I think the problems probably 
arise from the fact that (i) I am storing my trajectory as full 
precision .trr files and (ii) setting too small a value for nstxout and 
nstvout in .mdp. 
 
I have seen some tutorials that suggested using "trjconv" to derive the 
reduced precision .xtc files from the .trr files and then discard the 
latter. My question is, would this be wise as I am not sure whether I 
would find myself needing these .trr files in the future.
 


Then consider your objectives.  Does your intended analysis require full 
precision?  Do you need the velocities?  How many data points will you really 
need?  For the majority of analyses that one might perform, .xtc files suffice, 
so you can skip the .trr file altogether and write an .xtc file using nstxtcout.


Also of interest:

http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume

Here's a snippet of my .mdp file. Am I saving my coordinates and 
velocities too frequently? If I were to increase this, are there any 
compelling factors that I need to take into considerations?

; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 50; 2 * 50 = 1000 ps (1 ns)
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
 


I really see no need for such output every 0.2 ps.  I would consider 5000 data 
points per ns overkill for most applications.


-Justin


Many thanks for your help!
 
<<


Email has been scanned for viruses by UNMC email management service 



 >>



--


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] new beta release - gromacs-4.5-beta2

[Szilárd Páll]

Hi,

Could you provide the compiler versions you used? I really hope it's
not gcc 4.1.x again...

Cheers,
--
Szilárd



On Thu, Aug 5, 2010 at 8:26 PM, Elio Cino  wrote:
>
> Since the charmm force field has some instances with large charge groups
> (grompp warns you for it) it is advisable to use a longer cut-off (or no
> cut-off at all, by setting them all to 0). I've run 200 ns simulations  with
> 1.5 nm and nstlist = 5 and a timestep of 2 fs and constraints =  all-bonds.
>
> I could not have them set to infinite because I am using PBC. I used 1.5 and
> the system ran fine with 2fs timestep. On another note, I installed 4.5
> beta2 on another computer today and using the exact same system and settings
> I get tons of lincs errors (bond rotate over 30 deg) and cannot even do
> position restrain dynamics without segmentation fault. I even tried using
> the exact same tpr files as my successful runs.  The one that works was my
> laptop (OSX 10.6 core2 duo) and the one that fails is centos5 dual quad core
> xenon. If I run a normal solvated simulation, the linux machine runs fine.
>
> Elio Cino
>
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[gmx-users] GPU version does not support improper dihedrals?

[chris . neale]

This surprised me since most of the systems that I am interested in  
have improper dihedrals. Is it possible that I did something wrong here?


### Error message from mdrun-gpu:

Program mdrun-gpu, VERSION 4.0.99-dev-20100315
Source code file:  
/project/pomes/cneale/GPC/exe/intel/GPUgromacs/gromacs-4.5-beta2/src/kernel/openmm_wrapper.cpp, line:  
610


Fatal error:
OpenMM does not support (some) of the provided interaction type(s)  
(Improper Dih.)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


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[gmx-users] Re: phase shifts during dihedral fitting

[maria goranovic]

giving this a bump .. any suggestions please ?

On Mon, Aug 2, 2010 at 12:39 PM, maria goranovic
wrote:

> Friends
>
> Why are the phase shifts while making dihedral parameters always 0 or 180,
> for example near the unsaturated bond of a lipid ? I am trying to fit a
> function to a dihedral, and my phase shifts are more like 45 and 30 and 120
> degrees and the like. Is there any convenience behind using 0 or 180? How
> essential is that?
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>



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Copenhagen
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RE: [gmx-users] hyperthreading

[Berk Hess]

Hi,

These are nehalem Xeons I presume?
Then you get 15 to 20% more performance in Gromacs running 2 vs 1 thread or 
process per physical core.

Berk

> Date: Fri, 6 Aug 2010 09:24:11 -0500
> From: dmob...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] hyperthreading
> 
> Dear All,
> 
> I'm putting together a new Dell Xeon cluster running ROCKS 5.3 which
> uses CENTOS (6 I believe). This is currently ~20 dual quad-cores with
> roughly 16 GB of RAM each.
> 
> In any case, I wanted to inquire about hyperthreading. Does anyone
> have experience on similar machines with vs. without hyperthreading?
> The ROCKS users list suggests that hyperthreading ought always be off
> for HPC applications, which sounds overly simplistic to me, though I
> more or less follow the logic of this.
> 
> So, has anyone done any benchmarking yet in a similar setting, and
> what thoughts do you have? I obviously can do some benchmarking myself
> as well but I thought I'd check in with the list first.
> 
> Thanks so much,
> David
> 
> 
> -- 
> David Mobley
> dmob...@gmail.com
> 504-383-3662
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[gmx-users] hyperthreading

[David Mobley]

Dear All,

I'm putting together a new Dell Xeon cluster running ROCKS 5.3 which
uses CENTOS (6 I believe). This is currently ~20 dual quad-cores with
roughly 16 GB of RAM each.

In any case, I wanted to inquire about hyperthreading. Does anyone
have experience on similar machines with vs. without hyperthreading?
The ROCKS users list suggests that hyperthreading ought always be off
for HPC applications, which sounds overly simplistic to me, though I
more or less follow the logic of this.

So, has anyone done any benchmarking yet in a similar setting, and
what thoughts do you have? I obviously can do some benchmarking myself
as well but I thought I'd check in with the list first.

Thanks so much,
David


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Re: [gmx-users] pdb file

[Justin A. Lemkul]

leila karami wrote:

Hi gromacs users

I obtained pdb input file for gromacs from STRAP program. this pdb
file coantains protein and dna. this pdb file was obtaind form
superposition of 2 other pdb files. there is one problem: when I see
pdb file obtained from STRAP program by VMD, some bonds are
disappeared whereas when I open same file by text editor all things
are normal.as I can not attached this pdb file, I put residues 10-40
corresponding to protein from pdb.

please guide me


http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds

-Justin

--


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


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Re: [gmx-users] tests for gmx 4.5

[Rossen Apostolov]

 Hi Mark,

It will be definitely important to have the regressiontests working 
properly and extended as the development of Gromacs continues. We 
discussed that with Berk, and here are some suggestions about the 
structure of the suite.


1. Make all current tests 3.3.4 compliant. There _is_ actually such a 
release :) but it hasn't been really announced.


I put a link to the tarball on the website, but also if you checkout the 
releases-3-3-patches branch ,the release is the last commit in that 
branch: d26be1f4015d974530e8a203e08ade01008e56a8. The bugs that have 
been fixed since 3.3.3 are now on the website: 
http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_versions_3.x. 



Are there other important issues with that code?

2. There is not much point in comparing the tpr's themselves. Not only 
it becomes problematic with introducing new options etc, but most of all 
the important point is to make sure that the simulations are reproducible.


So instead, check the development binaries (mdrun-dev, grompp-dev etc.) 
like that:


   * run mdrun-dev first with the 3.3.4-reference.tpr and compare
 against 3.3.4-reference.trr/.edr
   * run grompp-dev to generate a new dev.tpr and
   * run mdrun-dev with dev.tpr and compare again against
 3.3.4-reference.trr/.edr

3. The above will check only features present in 3.3.4 (and before). New 
.tpr files will be needed for the new features available in later 
releases. But those will fail to run with older mdrun.


But that's OK - if the error is simply "reading tpx file (topol.tpr) 
version 71 with version 40 program", then the test will be skipped and 
reported as "N/A" instead of "Failed". In that way the suite can be run 
against any version of mdrun.


It might be better to limit the number of steps, lets say 50, but have 
stricter checking of the error. With longer runs the trajectories will 
start deviating more anyway.


Berk modified yesterday the way gmxcheck compares the virials - now it 
uses only the diagonal elements of the tensor since the relative 
tolerance is very different between them and the off-diagonal ones.


Also, the .mdp files should be as small as possible. All default values 
should be stripped to keep the input easy to read. I already did that 
with all grompp4.mdp files in the complex/ and simple/ tests (and 
removed the grompp.mdp files), the kernel/* ones are already using very 
slim inputs. I put the changes in a new branch, origin/temp_mdp, to keep 
the master clean before we decide what to do.


4. pdb2gmx: There are new FFs in 4.5 that were not present in previous 
version which should be checked also. Similarly to the mdrun checks, if 
pdb2gmx returns errors like "Library file ffamber99.rtp not found in 
current dir nor in default directories." (in 4.0) or "Could not find 
force field 'amber98'" (in 4.5), then skip the test and mark it as 
"N/A". EncadFF should be removed, and Amber/CHARMM tests added maybe a 
little later when we're sure the inputs are working fine.



Finally, when all the tests pass with 4.5 we can incorporate them within 
CTest (there is a very basic support at the moment) and we'll have a 
nice testing system:)


Any comments are welcome.
Rossen



On 8/4/10 6:08 PM, Mark Abraham wrote:
I'm glad there's some interest in the test set. I'm happy to update 
what I did for 4.0.7 for 4.5 also, but there are a number of issues 
that need attention from someone other than me. I listed those that 
occurred to me here 
http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.html, 
linked also from the Test Set page on the website.


Among those issues is that we need a single GROMACS version that 
produces reliable reference data for all cases we wish to test! 
Various of the 3.3.x series have known issues that make test set 
maintenance awkward.


If I do the necessary updates to release-3-3-patches branch to make a 
hypothetical GROMACS 3.3.4 that is useful for making test set 
reference calculations, should we make such a release? Alternatively, 
we can just announce that the reference data was generated by the 
3-3-version with a given git hash and not release. Thoughts?


Mark

- Original Message -
From: Rossen Apostolov 
Date: Wednesday, August 4, 2010 17:56
Subject: Re: [gmx-users] tests for gmx 4.5
To: gmx-users@gromacs.org

> Hi,
>
> The tests haven't been ported to 4.5 yet but I hope to fix that 
before the final release.

>
> Rossen
>
> On 7/31/10 7:08 PM, Alan wrote:

Is there a proper set of tests for gmx 4.5 because neither 
ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz or "git clone 
git://git.gromacs.org/regressiontests.git 
" is working due to the 
several modifications done in gmx 4.5 including automatic thread for 
mdrun (I am using a Mac with dual core) and more warnings.


> Thanks,
>
> Alan
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cam

Re: [gmx-users] compiling GPU 4.5b2, CUDA_INCLUDE_DIRECTORIES function is undefined

[Rossen Apostolov]

 Hi,

The GPU version uses the CUFFT libraries that come with CUDA, and no 
external or internal CPU libraries are actually being used. You can 
safely ignore the message.


Rossen

On 8/6/10 9:31 PM, chris.ne...@utoronto.ca wrote:

Thank you Rossen, that worked.

When I compile, should I be including my FFTW as per normal? I didn't 
do that since it was not mentioned and during the build, I get "-- 
Using internal FFT library - fftpack"


--- original message ---

  Hi Chris,


## what I did:

module purge
module load gcc/gcc-4.4.0
module load cmake/2.8.0  #need version >=2.6.4
module load cuda/cuda-3.1
mkdir gpuexec
export 
OPENMM_ROOT_DIR=/project/pomes/cneale/GPC/exe/OpenMM2.0-Source/exec/openmm
cmake /project/pomes/cneale/GPC/exe/intel/gromacs-4.5-beta2/*src* 
-DGMX_OPENMM=ON

Here is the problem - you are passing to CMake the wrong path, it should
be just /project/pomes/cneale/GPC/exe/intel/gromacs-4.5-beta2/ (rather
than ...-beta2/*src*)
-DGMX_THREADS=OFF -DCMAKE_INSTALL_PREFIX=$(pwd)/gpuexec 
-DLIB_INSTALL_DIR=$(pwd)/gpuexec


## output

CMake Error at kernel/gmx_gpu_utils/CMakeLists.txt:18 
(CUDA_INCLUDE_DIRECTORIES):

  Unknown CMake command "CUDA_INCLUDE_DIRECTORIES".






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Re: [gmx-users] tests for gmx 4.5

[Rossen Apostolov]

 Hi,
I'm resending the message below from last week because it didn't make it 
to the list due to some problem with the server.

Rossen

-

Hi Mark,

It will be definitely important to have the regressiontests working 
properly and extended as the development of Gromacs continues. We 
discussed that with Berk, and here are some suggestions about the 
structure of the suite.


1. Make all current tests 3.3.4 compliant. There _is_ actually such a 
release :) but it hasn't been really announced.


I put a link to the tarball on the website, but also if you checkout the 
releases-3-3-patches branch ,the release is the last commit in that 
branch: d26be1f4015d974530e8a203e08ade01008e56a8. The bugs that have 
been fixed since 3.3.3 are now on the website: 
http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_versions_3.x. 



Are there other important issues with that code?

2. There is not much point in comparing the tpr's themselves. Not only 
it becomes problematic with introducing new options etc, but most of all 
the important point is to make sure that the simulations are reproducible.


So instead, check the development binaries (mdrun-dev, grompp-dev etc.) 
like that:


   * run mdrun-dev first with the 3.3.4-reference.tpr and compare
 against 3.3.4-reference.trr/.edr
   * run grompp-dev to generate a new dev.tpr and
   * run mdrun-dev with dev.tpr and compare again against
 3.3.4-reference.trr/.edr

3. The above will check only features present in 3.3.4 (and before). New 
.tpr files will be needed for the new features available in later 
releases. But those will fail to run with older mdrun.


But that's OK - if the error is simply "reading tpx file (topol.tpr) 
version 71 with version 40 program", then the test will be skipped and 
reported as "N/A" instead of "Failed". In that way the suite can be run 
against any version of mdrun.


It might be better to limit the number of steps, lets say 50, but have 
stricter checking of the error. With longer runs the trajectories will 
start deviating more anyway.


Berk modified yesterday the way gmxcheck compares the virials - now it 
uses only the diagonal elements of the tensor since the relative 
tolerance is very different between them and the off-diagonal ones.


Also, the .mdp files should be as small as possible. All default values 
should be stripped to keep the input easy to read. I already did that 
with all grompp4.mdp files in the complex/ and simple/ tests (and 
removed the grompp.mdp files), the kernel/* ones are already using very 
slim inputs. I put the changes in a new branch, origin/temp_mdp, to keep 
the master clean before we decide what to do.


4. pdb2gmx: There are new FFs in 4.5 that were not present in previous 
version which should be checked also. Similarly to the mdrun checks, if 
pdb2gmx returns errors like "Library file ffamber99.rtp not found in 
current dir nor in default directories." (in 4.0) or "Could not find 
force field 'amber98'" (in 4.5), then skip the test and mark it as 
"N/A". EncadFF should be removed, and Amber/CHARMM tests added maybe a 
little later when we're sure the inputs are working fine.



Finally, when all the tests pass with 4.5 we can incorporate them within 
CTest (there is a very basic support at the moment) and we'll have a 
nice testing system:)


Any comments are welcome.
Rossen



On 8/4/10 6:08 PM, Mark Abraham wrote:
I'm glad there's some interest in the test set. I'm happy to update 
what I did for 4.0.7 for 4.5 also, but there are a number of issues 
that need attention from someone other than me. I listed those that 
occurred to me here 
http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.html, 
linked also from the Test Set page on the website.


Among those issues is that we need a single GROMACS version that 
produces reliable reference data for all cases we wish to test! 
Various of the 3.3.x series have known issues that make test set 
maintenance awkward.


If I do the necessary updates to release-3-3-patches branch to make a 
hypothetical GROMACS 3.3.4 that is useful for making test set 
reference calculations, should we make such a release? Alternatively, 
we can just announce that the reference data was generated by the 
3-3-version with a given git hash and not release. Thoughts?


Mark

- Original Message -
From: Rossen Apostolov 
Date: Wednesday, August 4, 2010 17:56
Subject: Re: [gmx-users] tests for gmx 4.5
To: gmx-users@gromacs.org

> Hi,
>
> The tests haven't been ported to 4.5 yet but I hope to fix that 
before the final release.

>
> Rossen
>
> On 7/31/10 7:08 PM, Alan wrote:

Is there a proper set of tests for gmx 4.5 because neither 
ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz or "git clone 
git://git.gromacs.org/regressiontests.git 
" is working due to the 
several modifications done in gmx 4.5 including automatic thread for 
mdrun (I am using a Mac with d

[gmx-users] Re: Constraints between multiple molecules

[Michael McGovern]

Thanks a lot for the help, that will do well enough, but require me to redo 
some things I did before.  As far as you know there is no way to have multiple 
constraints using the center masses of the peptides?  Thanks.

_One thing which you could do is to write your three proteins into 
one molecule definition (if you use .itp files, then make one .itp for 
all three). Then at the end of the molecule definition you can add 
the constraints.
To merge the three proteins is rather easy but cumbersome, you must shift all 
the atom numbers of the second and third protein. So if each protein would have 
100 atoms, protein2 would start with atom 101. depending how big your proteins 
are it could be better to write a script which merges the three proteins 
instead of doing it by hand.

Greetings
Thomas
___Or just re-create the topology with pdb2gmx -merge.

-Justin

___


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[gmx-users] abnormal stop of job

[chris . neale]

This sounds like you, or your sysadmin, killed the job. It is also  
possible if you are using a cluster that there is a walltime limit and  
you exceeded that, so your job was sent the term signal.


You should restart the run. Check the manual on how to do that since  
it depends on what version of gromacs you are using.


I sent a mail like this a few hours ago, but it didn;t seem to go  
through, so I am resending.


Chris.

-- original message --

Hi all,
  I have been running a simulation of 200 ns length and it suddenly
stoped at 67 ns showing the following line -

Received the TERM signal, stopping at the next step

I have checked the time steps properly and there is no error. What should I do
now? Please suggest.

Thanks


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[gmx-users] Test

[Justin A. Lemkul]

My messages haven't been going through since yesterday, testing to see if this 
one makes it.


--


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] compiling GPU 4.5b2, CUDA_INCLUDE_DIRECTORIES function is undefined

[chris . neale]

Thank you Rossen, that worked.

When I compile, should I be including my FFTW as per normal? I didn't  
do that since it was not mentioned and during the build, I get "--  
Using internal FFT library - fftpack"


--- original message ---

  Hi Chris,


## what I did:

module purge
module load gcc/gcc-4.4.0
module load cmake/2.8.0  #need version >=2.6.4
module load cuda/cuda-3.1
mkdir gpuexec
export  
OPENMM_ROOT_DIR=/project/pomes/cneale/GPC/exe/OpenMM2.0-Source/exec/openmm
cmake /project/pomes/cneale/GPC/exe/intel/gromacs-4.5-beta2/*src*  
-DGMX_OPENMM=ON

Here is the problem - you are passing to CMake the wrong path, it should
be just /project/pomes/cneale/GPC/exe/intel/gromacs-4.5-beta2/ (rather
than ...-beta2/*src*)
-DGMX_THREADS=OFF -DCMAKE_INSTALL_PREFIX=$(pwd)/gpuexec  
-DLIB_INSTALL_DIR=$(pwd)/gpuexec


## output

CMake Error at kernel/gmx_gpu_utils/CMakeLists.txt:18  
(CUDA_INCLUDE_DIRECTORIES):

  Unknown CMake command "CUDA_INCLUDE_DIRECTORIES".




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[gmx-users] Test

[Rossen Apostolov]

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