[gmx-users] Re: Velocity autocorrelation function of water using g_velacc

[Vitaly Chaban]

Generally, hydrogen-bonded liquids exhibits more complexed velocity
autocorrelations than others... I recollect something like that,
working with methanol.



On Mon, May 23, 2011 at 4:23 PM, Vitaly Chaban  wrote:
> Andrew,
>
> Look here: http://www.sciencedirect.com/science/article/pii/S0022286004002765
>
> I believe the VACs there are the same that you've showed us. So, you
> are on the safe side, as for me.
>
> --
> Dr. Vitaly V. Chaban, Department of Chemistry
> University of Rochester, Rochester, New York 14627-0216
>
>
>
>> If you have time, could you please look at my result at
>> http://www.andrew.cmu.edu/user/adeyoung/velacc_may23.pdf and see if you
>> think it is a qualitatively reasonable result?  My main concern is the first
>> local minimum, which I have labeled with an arrow on the plot.  This minimum
>> is in the _positive_ regime, which I believe (but I am not sure) cannot
>> correspond to the recoil of atoms when they collide.
>>
>> In my pdf file I have displayed the parameters I have used for equilibration
>> and dynamics.  To summarize, I have used the leap frog algorithm with 2 ns
>> equilibration in 1 fs steps, and 5 ns dynamics in 1 fs steps.  For dynamics,
>> I have saved configurations every 2 fs.  Although my result from g_velacc
>> has velocity autocorrelation frunction data from 0 to 1000 ps, the function
>> decays rapidly to zero (as it should, I think, because the velocity rapidly
>> decorrelates since the atoms/molecules "forget" their initial velocities),
>> so I have plotted only from 0 to 1 ps.  I am running Gromacs version 4.5.4.
>



-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: Velocity autocorrelation function of water using g_velacc

[Vitaly Chaban]

Andrew,

Look here: http://www.sciencedirect.com/science/article/pii/S0022286004002765

I believe the VACs there are the same that you've showed us. So, you
are on the safe side, as for me.

-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216



> If you have time, could you please look at my result at
> http://www.andrew.cmu.edu/user/adeyoung/velacc_may23.pdf and see if you
> think it is a qualitatively reasonable result?  My main concern is the first
> local minimum, which I have labeled with an arrow on the plot.  This minimum
> is in the _positive_ regime, which I believe (but I am not sure) cannot
> correspond to the recoil of atoms when they collide.
>
> In my pdf file I have displayed the parameters I have used for equilibration
> and dynamics.  To summarize, I have used the leap frog algorithm with 2 ns
> equilibration in 1 fs steps, and 5 ns dynamics in 1 fs steps.  For dynamics,
> I have saved configurations every 2 fs.  Although my result from g_velacc
> has velocity autocorrelation frunction data from 0 to 1000 ps, the function
> decays rapidly to zero (as it should, I think, because the velocity rapidly
> decorrelates since the atoms/molecules "forget" their initial velocities),
> so I have plotted only from 0 to 1 ps.  I am running Gromacs version 4.5.4.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8

[Justin A. Lemkul]

Peter C. Lai wrote:

On 2011-05-23 02:37:54PM -0500, Matthew Bick wrote:

Dear Gromacs community.  I am attempting to install the latest version
of Gromcs (4.5.4) on my Mac Powerbook G4 (1.67 MHz, OS 10.5.8).  I
have successfully installed FFTW following the instructions provided
on the Gromacs installation page.

"./configure --with-fft=fftw3" appears to work properly, but when I
perform  "Make" I get the following errors:

ld: symbol(s) not found
collect2: ld returned 1 exit status
make[4]: *** [libgmx.la] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1

I did configure my shell (bash) environment, as per the Gromacs
installation instructions.  "Make" runs for about 10 minutes before I
get these errors.  I have searched the mailing list, and have seen
people report problems similar to mine, but couldn't determine how
those problems were resolved.  Also from the mailing list, I
understand that the errors I've listed above aren't that informative.
If it helps, I repeatedly get the following warnings during "Make":

../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
function ‘tMPI_Atomic_add_return’:
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:46:
warning: implicit declaration of function ‘__sync_add_and_fetch’
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
function ‘tMPI_Atomic_fetch_add’:
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:51:
warning: implicit declaration of function ‘__sync_fetch_and_add’
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
function ‘tMPI_Atomic_cas’:
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57:
warning: implicit declaration of function
‘__sync_bool_compare_and_swap’

If anyone has any suggestions, they would be greatly appreciated.
Thanks.



Some things to watch out for:
single vs. double precision (the library versions must match between
fftw and what you passed to ./configure for gromacs (--enable-float
is single precision,--disable-float is double).



If incorrect FFTW libraries were found, configuration would have failed.


Maybe you need --enable-shared and specify correct LDFLAGS...
The warnings section seems to imply this is happening in the threads/MPI
section, Justin can correct me if I'm wrong, but maybe you need to explicitly
disable mpi with --disable-mpi in the configure?



The thread_mpi library corresponds to the internal threading built into Gromacs 
and doesn't have anything to do with external MPI libraries.  The --disable-mpi 
option is the default behavior, anyway, and is only used in case of an MPI 
(non-threading) build.  It is worth noting that in a single installation step, 
threading and MPI cannot be mixed; you use one or the other.  A full 
configuration command would be necessary to see what's going on.


-Justin

Gromacs 4.5.4 is also in MacPorts, which contains a simplified options 
framework (and will install gcc45 for you if you want as well) for all the

popular configure variations:
http://www.macports.org/ports.php?by=name&substr=gromacs
(I would probably go with +gcc45, +gsl, +no_x11 [avoids openmotif]
and +optimize [for gsl])

Once you do get it working, watchout for overheating on that thing :)



--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8

[Peter C. Lai]

On 2011-05-23 02:37:54PM -0500, Matthew Bick wrote:
> Dear Gromacs community.  I am attempting to install the latest version
> of Gromcs (4.5.4) on my Mac Powerbook G4 (1.67 MHz, OS 10.5.8).  I
> have successfully installed FFTW following the instructions provided
> on the Gromacs installation page.
> 
> "./configure --with-fft=fftw3" appears to work properly, but when I
> perform  "Make" I get the following errors:
> 
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
> make[4]: *** [libgmx.la] Error 1
> make[3]: *** [all-recursive] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all] Error 2
> make: *** [all-recursive] Error 1
> 
> I did configure my shell (bash) environment, as per the Gromacs
> installation instructions.  "Make" runs for about 10 minutes before I
> get these errors.  I have searched the mailing list, and have seen
> people report problems similar to mine, but couldn't determine how
> those problems were resolved.  Also from the mailing list, I
> understand that the errors I've listed above aren't that informative.
> If it helps, I repeatedly get the following warnings during "Make":
> 
> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
> function ‘tMPI_Atomic_add_return’:
> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:46:
> warning: implicit declaration of function ‘__sync_add_and_fetch’
> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
> function ‘tMPI_Atomic_fetch_add’:
> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:51:
> warning: implicit declaration of function ‘__sync_fetch_and_add’
> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
> function ‘tMPI_Atomic_cas’:
> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57:
> warning: implicit declaration of function
> ‘__sync_bool_compare_and_swap’
> 
> If anyone has any suggestions, they would be greatly appreciated.
> Thanks.
> 

Some things to watch out for:
single vs. double precision (the library versions must match between
fftw and what you passed to ./configure for gromacs (--enable-float
is single precision,--disable-float is double).

Maybe you need --enable-shared and specify correct LDFLAGS...
The warnings section seems to imply this is happening in the threads/MPI
section, Justin can correct me if I'm wrong, but maybe you need to explicitly
disable mpi with --disable-mpi in the configure?

Gromacs 4.5.4 is also in MacPorts, which contains a simplified options 
framework (and will install gcc45 for you if you want as well) for all the
popular configure variations:
http://www.macports.org/ports.php?by=name&substr=gromacs
(I would probably go with +gcc45, +gsl, +no_x11 [avoids openmotif]
and +optimize [for gsl])

Once you do get it working, watchout for overheating on that thing :)

-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8

[Justin A. Lemkul]

Matthew Bick wrote:

Dear Gromacs community.  I am attempting to install the latest version
of Gromcs (4.5.4) on my Mac Powerbook G4 (1.67 MHz, OS 10.5.8).  I
have successfully installed FFTW following the instructions provided
on the Gromacs installation page.

"./configure --with-fft=fftw3" appears to work properly, but when I
perform  "Make" I get the following errors:

ld: symbol(s) not found
collect2: ld returned 1 exit status
make[4]: *** [libgmx.la] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1



The information about the actual missing symbols should be just above this 
output, so that would be useful information.  Also pertinent would be the 
compiler versions you're using.  From what you've posted below it looks like 
GCC, but which version?


I don't think those warnings are particularly harmful, but I know that trying to 
install a new version of Gromacs on PowerPC can be a challenge.  If your 
compiler is relatively old, you may have to disable some of the newer features, 
like threading, although that should have been caught during configuration.


Is the ./configure command given above the exact command you used?  If not, 
posting that would be useful.


-Justin


I did configure my shell (bash) environment, as per the Gromacs
installation instructions.  "Make" runs for about 10 minutes before I
get these errors.  I have searched the mailing list, and have seen
people report problems similar to mine, but couldn't determine how
those problems were resolved.  Also from the mailing list, I
understand that the errors I've listed above aren't that informative.
If it helps, I repeatedly get the following warnings during "Make":

../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
function ‘tMPI_Atomic_add_return’:
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:46:
warning: implicit declaration of function ‘__sync_add_and_fetch’
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
function ‘tMPI_Atomic_fetch_add’:
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:51:
warning: implicit declaration of function ‘__sync_fetch_and_add’
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
function ‘tMPI_Atomic_cas’:
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57:
warning: implicit declaration of function
‘__sync_bool_compare_and_swap’

If anyone has any suggestions, they would be greatly appreciated.
Thanks.

Matthew Bick
Rockefeller University


--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8

[Matthew Bick]

Dear Gromacs community.  I am attempting to install the latest version
of Gromcs (4.5.4) on my Mac Powerbook G4 (1.67 MHz, OS 10.5.8).  I
have successfully installed FFTW following the instructions provided
on the Gromacs installation page.

"./configure --with-fft=fftw3" appears to work properly, but when I
perform  "Make" I get the following errors:

ld: symbol(s) not found
collect2: ld returned 1 exit status
make[4]: *** [libgmx.la] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1

I did configure my shell (bash) environment, as per the Gromacs
installation instructions.  "Make" runs for about 10 minutes before I
get these errors.  I have searched the mailing list, and have seen
people report problems similar to mine, but couldn't determine how
those problems were resolved.  Also from the mailing list, I
understand that the errors I've listed above aren't that informative.
If it helps, I repeatedly get the following warnings during "Make":

../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
function ‘tMPI_Atomic_add_return’:
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:46:
warning: implicit declaration of function ‘__sync_add_and_fetch’
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
function ‘tMPI_Atomic_fetch_add’:
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:51:
warning: implicit declaration of function ‘__sync_fetch_and_add’
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
function ‘tMPI_Atomic_cas’:
../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57:
warning: implicit declaration of function
‘__sync_bool_compare_and_swap’

If anyone has any suggestions, they would be greatly appreciated.
Thanks.

Matthew Bick
Rockefeller University
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Velocity autocorrelation function of water using g_velacc

[David van der Spoel]

On 2011-05-23 20.52, Justin A. Lemkul wrote:



Andrew DeYoung wrote:

Hi,
I have run a simulation of 254 SPC/E water molecules in a cubic box of
edge
length 19.660 Angstrom. I have used the gromacs utility g_velacc to
calculate the velocity autocorrelation function for the motion of only
the
oxygen atoms. When I plot the velocity autocorrelation function versus
time, my result is a curve with more than one local minimum.
My question is, should I expect having more than one local minimum? I am
not sure that my result is reasonable.

For example, the Democritus molecular dynamics website gives one
example of
a velocity autocorrelation function, although they do not specifically
say
what system (water or something else?) or what state (liquid or gas?) was
used:
http://www.cse.scitech.ac.uk/ccg/software/Democritus/Theory/vaf.html .
Their plot shows one "strong" local minimum and one "weaker" one; both of
these local minima are in the negative regime. I am new to this field,
but
I believe that the "strong" local minimum corresponds conceptually to the
recoil of the atoms when they collide.
If you have time, could you please look at my result at
http://www.andrew.cmu.edu/user/adeyoung/velacc_may23.pdf and see if you
think it is a qualitatively reasonable result? My main concern is the
first
local minimum, which I have labeled with an arrow on the plot. This
minimum
is in the _positive_ regime, which I believe (but I am not sure) cannot
correspond to the recoil of atoms when they collide.
In my pdf file I have displayed the parameters I have used for
equilibration
and dynamics. To summarize, I have used the leap frog algorithm with 2 ns
equilibration in 1 fs steps, and 5 ns dynamics in 1 fs steps. For
dynamics,
I have saved configurations every 2 fs. Although my result from g_velacc
has velocity autocorrelation frunction data from 0 to 1000 ps, the
function
decays rapidly to zero (as it should, I think, because the velocity
rapidly
decorrelates since the atoms/molecules "forget" their initial
velocities),
so I have plotted only from 0 to 1 ps. I am running Gromacs version
4.5.4.




I don't know if this explains your result or not, but you do realize
that if you have "gen_vel = yes" at the beginning of your simulation for
data collection, it negates any value in previous equilibration, right?
You've destroyed the ensemble you created before. You should pass the
checkpoint file from the equilibration run to grompp -t and set "gen_vel
= no" for your simulation. I'd start by doing that and seeing if it
affects the result, because at this point, it may just be that you
haven't properly re-equilibrated, or at the very least, the original
frames are messing with the VACF calculation.

-Justin


Or you can just omit the first 100 ps from the analysis.
There can be multiple minima, not a problem. If you integrate the VACF 
you should get the diffusion constant (3D), check manual and compare to 
g_msd.


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Velocity autocorrelation function of water using g_velacc

[Justin A. Lemkul]

Andrew DeYoung wrote:
Hi, 


I have run a simulation of 254 SPC/E water molecules in a cubic box of edge
length 19.660 Angstrom.  I have used the gromacs utility g_velacc to
calculate the velocity autocorrelation function for the motion of only the
oxygen atoms.  When I plot the velocity autocorrelation function versus
time, my result is a curve with more than one local minimum.  


My question is, should I expect having more than one local minimum?  I am
not sure that my result is reasonable.

For example, the Democritus molecular dynamics website gives one example of
a velocity autocorrelation function, although they do not specifically say
what system (water or something else?) or what state (liquid or gas?) was
used: http://www.cse.scitech.ac.uk/ccg/software/Democritus/Theory/vaf.html .
Their plot shows one "strong" local minimum and one "weaker" one; both of
these local minima are in the negative regime.  I am new to this field, but
I believe that the "strong" local minimum corresponds conceptually to the
recoil of the atoms when they collide.  


If you have time, could you please look at my result at
http://www.andrew.cmu.edu/user/adeyoung/velacc_may23.pdf and see if you
think it is a qualitatively reasonable result?  My main concern is the first
local minimum, which I have labeled with an arrow on the plot.  This minimum
is in the _positive_ regime, which I believe (but I am not sure) cannot
correspond to the recoil of atoms when they collide.  


In my pdf file I have displayed the parameters I have used for equilibration
and dynamics.  To summarize, I have used the leap frog algorithm with 2 ns
equilibration in 1 fs steps, and 5 ns dynamics in 1 fs steps.  For dynamics,
I have saved configurations every 2 fs.  Although my result from g_velacc
has velocity autocorrelation frunction data from 0 to 1000 ps, the function
decays rapidly to zero (as it should, I think, because the velocity rapidly
decorrelates since the atoms/molecules "forget" their initial velocities),
so I have plotted only from 0 to 1 ps.  I am running Gromacs version 4.5.4.




I don't know if this explains your result or not, but you do realize that if you 
have "gen_vel = yes" at the beginning of your simulation for data collection, it 
negates any value in previous equilibration, right?  You've destroyed the 
ensemble you created before.  You should pass the checkpoint file from the 
equilibration run to grompp -t and set "gen_vel = no" for your simulation.  I'd 
start by doing that and seeing if it affects the result, because at this point, 
it may just be that you haven't properly re-equilibrated, or at the very least, 
the original frames are messing with the VACF calculation.


-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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Velocity autocorrelation function of water using g_velacc

[Andrew DeYoung]

Hi, 

I have run a simulation of 254 SPC/E water molecules in a cubic box of edge
length 19.660 Angstrom.  I have used the gromacs utility g_velacc to
calculate the velocity autocorrelation function for the motion of only the
oxygen atoms.  When I plot the velocity autocorrelation function versus
time, my result is a curve with more than one local minimum.  

My question is, should I expect having more than one local minimum?  I am
not sure that my result is reasonable.

For example, the Democritus molecular dynamics website gives one example of
a velocity autocorrelation function, although they do not specifically say
what system (water or something else?) or what state (liquid or gas?) was
used: http://www.cse.scitech.ac.uk/ccg/software/Democritus/Theory/vaf.html .
Their plot shows one "strong" local minimum and one "weaker" one; both of
these local minima are in the negative regime.  I am new to this field, but
I believe that the "strong" local minimum corresponds conceptually to the
recoil of the atoms when they collide.  

If you have time, could you please look at my result at
http://www.andrew.cmu.edu/user/adeyoung/velacc_may23.pdf and see if you
think it is a qualitatively reasonable result?  My main concern is the first
local minimum, which I have labeled with an arrow on the plot.  This minimum
is in the _positive_ regime, which I believe (but I am not sure) cannot
correspond to the recoil of atoms when they collide.  

In my pdf file I have displayed the parameters I have used for equilibration
and dynamics.  To summarize, I have used the leap frog algorithm with 2 ns
equilibration in 1 fs steps, and 5 ns dynamics in 1 fs steps.  For dynamics,
I have saved configurations every 2 fs.  Although my result from g_velacc
has velocity autocorrelation frunction data from 0 to 1000 ps, the function
decays rapidly to zero (as it should, I think, because the velocity rapidly
decorrelates since the atoms/molecules "forget" their initial velocities),
so I have plotted only from 0 to 1 ps.  I am running Gromacs version 4.5.4.


Thank you very much for your time.

Andrew DeYoung
Carnegie Mellon University

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Error in energy group exclusion

[Justin A. Lemkul]

bipin singh wrote:

Thanks for your reply,
I have already done with the final simulation, and now if I have to
change the method for electrostatic calculation(instead of PME)
for energy group exclusion, then will it make sense i.e. how
consistent it would be with my simulation results(with PME).
Please suggest..



I'm not 100% clear on what you're doing, but I assume you're trying to do some 
rerun of a trajectory to calculate various energy components?  If that's the 
case, there is a wealth of discussion on this topic in the list archive.  It is 
generally an exercise in futility or ambiguity.  If a trajectory was generated 
using long-range methods like PME, what sense is it to re-calculate some 
component of the the energies of configurations that were created using a 
different method?  The long-range terms may have a significant impact on the 
dynamical behavior, which you're now ignoring.


If this is not your intent, then please explain further.

-Justin


On Mon, May 23, 2011 at 21:28, Justin A. Lemkul  wrote:


bipin singh wrote:

Hello users,
I am getting the following warning during the grompp

-
WARNING 1 [file md.mdp]:
 Can not exclude the lattice Coulomb energy between energy groups

---

I am providing the following energy groups and  energy exclusion group
in my mdp file
energygrps=Protein SOL
energygrp_excl=Protein Protein SOL SOL

Please suggest me, why I am getting the above error and how to get rid
of this error.


Presumably you're using PME for long-range electrostatics.  The message
you're getting is grompp trying to help you realize that with PME it is not
possible to completely exclude all energetic terms, since the long-range
mesh is always calculated.  Only short-range nonbonded interactions (LJ and
Coulombic terms) are excluded in the mechanism above.

-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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists







--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] compressing with NPT

[Peter C. Lai]

On 2011-05-23 11:02:46AM -0500, Elisabeth wrote:
> Dear experts,
> 
> I have been considering effect of fixing bond lengths in my system 
> (constraints= none / all-bonds) on equilibrated density using NPT runs with 
> 4.5.4. I am showing two set of results for two ref pressures of 10 and 70 
> bar. in case of constraints= none I had to employ a 0.5 fs timestep otherwise 
> system blows up. Can you please comment why equilibrated densities are 
> different for the same reference pressure? Thanks.
> 
> 70 bar, all bonds constraint
> timestep 2fs
> 
> Statistics over 875001 steps [ 250. through 2000. ps ], 2 data sets
> All statistics are over 87501 points
> 
> Energy  Average   Err.Est.   RMSD  Tot-Drift
> ---
> Pressure70.4993  0.092542.944   0.222707  (bar)
> Density 625.894   0.3911.9075   0.110708  (kg/m^3)
> 
> 
> 70 bar, constraints= none
> timestep 0.5 fs
> 
> Statistics over 351 steps [ 250. through 2000. ps ], 2 data sets
> All statistics are over 350001 points
> 
> Energy  Average   Err.Est.   RMSD  Tot-Drift
> ---
> Pressure70.6207   0.11932.219  -0.500892  (bar)
> Density 614.451   0.5513.7381  -0.347349  (kg/m^3)
> 
> 
> ---
> 
> 10 bar, all bonds constraint
> timestep 2fs
> 
> Statistics over 875001 steps [ 250. through 2000. ps ], 2 data sets
> All statistics are over 87501 points
> 
> Energy  Average   Err.Est.   RMSD  Tot-Drift
> ---
> Pressure10.4843  0.039621.684  0.0156492  (bar)
> Density 624.362  112.1354   -2.11725  (kg/m^3)
> 
> 
> 10 bar, constraints= none
> timestep 0.5 fs
> 
> Statistics over 51 steps [ 250. through 500. ps ], 2 data sets
> All statistics are over 50001 points
> 
> Energy  Average   Err.Est.   RMSD  Tot-Drift
> ---
> Temperature  299.92   0.114.86352  -0.139097  (K)
> Density 600.689  214.759711.6485  (kg/m^3)
> 

A couple of questions:

First, what is your criteria that your system has equilibrated? Have you run
longer to see if density stabilizes or plotted the g_energy to see if it has
periodicized after 2ns?

Second, in your 10bar comparisons, you have compared a 2ns run with a 500ps
run, and you can see that after 500ps the density drift over that time was 
11.6kg/m3, making it seem like it is still not in equlibrium.

Finally, are the differences in density statistically significant compared
to an expectant value? i.e. 10kg/m3 difference may or may not be significant 
at 70bar for a system of your size especially if you started at "only" 7nm 
per side and you have compressed it so much more...

Anecdotally, I have found that my own system, "compressing" to a normal 1atm
(from NVT to NPT) seems to converge faster (over the same timescale) with 
constraints = h-bond vs. constraints = all-bonds, but I do have long heavy
atom connectivities...

-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: compressing with NPT

[Vitaly Chaban]

Because when you introduce constraints, you change the model. Why is
it strange for you, I would ask.

Meanwhile, the difference is comparable with RMSD.


-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216




> Dear experts,
>
> I have been considering effect of fixing bond lengths in my system
> (constraints= none / all-bonds) on equilibrated density using NPT runs with
> 4.5.4. I am showing two set of results for two ref pressures of 10 and 70
> bar. in case of constraints= none I had to employ a 0.5 fs timestep
> otherwise system blows up. Can you please comment why equilibrated densities
> are different for the same reference pressure? Thanks.
>
> 70 bar, all bonds constraint
> timestep 2fs
>
> Statistics over 875001 steps [ 250. through 2000. ps ], 2 data sets
> All statistics are over 87501 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> ---
> Pressure                    70.4993      0.092    542.944   0.222707  (bar)
> Density                     625.894       0.39    11.9075   0.110708
> (kg/m^3)
>
>
> 70 bar, constraints= none
> timestep 0.5 fs
>
> Statistics over 351 steps [ 250. through 2000. ps ], 2 data sets
> All statistics are over 350001 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> ---
> Pressure                    70.6207       0.11    932.219  -0.500892  (bar)
> Density                     614.451       0.55    13.7381  -0.347349
> (kg/m^3)
>
>
> ---
>
> 10 bar, all bonds constraint
> timestep 2fs
>
> Statistics over 875001 steps [ 250. through 2000. ps ], 2 data sets
> All statistics are over 87501 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> ---
> Pressure                    10.4843      0.039    621.684  0.0156492  (bar)
> Density                     624.362          1    12.1354   -2.11725
> (kg/m^3)
>
>
> 10 bar, constraints= none
> timestep 0.5 fs
>
> Statistics over 51 steps [ 250. through 500. ps ], 2 data sets
> All statistics are over 50001 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> ---
> Temperature                  299.92       0.11    4.86352  -0.139097  (K)
> Density                     600.689          2    14.7597    11.6485
> (kg/m^3)
>
>
> ;        Run control
> integrator          =  md
> dt                  =  0.002         ; 0.0005 for constraints =none
> otherwise blows up
> nsteps              =  100
> nstcomm             =  100
>
> ;        Output control
> nstenergy           =  100
> nstxout             =  100
> nstvout             =  0
> nstfout             =  0
> nstlog              =  1000
> nstxtcout          =  1000
>
> ;        Neighbor searching
> nstlist             =  10
> ns_type             =  grid
>
> ;        Electrostatics/VdW
> coulombtype         =  shift
> vdw-type            =  Shift
> rcoulomb-switch     =  0
> rvdw-switch         =  0.9
>
> ;        Cut-offs
> rlist               =  1.25
> rcoulomb            =  1.0
> rvdw                =  1.0
>
>
> ;        Temperature coupling
> Tcoupl              =  v-rescale
> tc-grps             =  System
> tau_t               =  0.1
> ref_t               =  300
>
> ;        Pressure coupling
> Pcoupl              =  Parrinello-Rahman
> Pcoupltype          =  isotropic
> tau_p               =  2
> compressibility     =  4.5e-5 4.5e-5
> ref_p               =  10
>
> constraints             = all-bonds
> constraint-algorithm = lincs
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Error in energy group exclusion

[bipin singh]

Thanks for your reply,
I have already done with the final simulation, and now if I have to
change the method for electrostatic calculation(instead of PME)
for energy group exclusion, then will it make sense i.e. how
consistent it would be with my simulation results(with PME).
Please suggest..

On Mon, May 23, 2011 at 21:28, Justin A. Lemkul  wrote:
>
>
> bipin singh wrote:
>>
>> Hello users,
>> I am getting the following warning during the grompp
>>
>> -
>> WARNING 1 [file md.mdp]:
>>  Can not exclude the lattice Coulomb energy between energy groups
>>
>> ---
>>
>> I am providing the following energy groups and  energy exclusion group
>> in my mdp file
>> energygrps=Protein SOL
>> energygrp_excl=Protein Protein SOL SOL
>>
>> Please suggest me, why I am getting the above error and how to get rid
>> of this error.
>>
>
> Presumably you're using PME for long-range electrostatics.  The message
> you're getting is grompp trying to help you realize that with PME it is not
> possible to completely exclude all energetic terms, since the long-range
> mesh is always calculated.  Only short-range nonbonded interactions (LJ and
> Coulombic terms) are excluded in the mechanism above.
>
> -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
>
> 
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
---
Regards,
Bipin Singh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] compressing with NPT

[Elisabeth]

Dear experts,

I have been considering effect of fixing bond lengths in my system
(constraints= none / all-bonds) on equilibrated density using NPT runs with
4.5.4. I am showing two set of results for two ref pressures of 10 and 70
bar. in case of constraints= none I had to employ a 0.5 fs timestep
otherwise system blows up. Can you please comment why equilibrated densities
are different for the same reference pressure? Thanks.

70 bar, all bonds constraint
timestep 2fs

Statistics over 875001 steps [ 250. through 2000. ps ], 2 data sets
All statistics are over 87501 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure70.4993  0.092542.944   0.222707  (bar)
Density 625.894   0.3911.9075   0.110708
(kg/m^3)


70 bar, constraints= none
timestep 0.5 fs

Statistics over 351 steps [ 250. through 2000. ps ], 2 data sets
All statistics are over 350001 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure70.6207   0.11932.219  -0.500892  (bar)
Density 614.451   0.5513.7381  -0.347349
(kg/m^3)


---

10 bar, all bonds constraint
timestep 2fs

Statistics over 875001 steps [ 250. through 2000. ps ], 2 data sets
All statistics are over 87501 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure10.4843  0.039621.684  0.0156492  (bar)
Density 624.362  112.1354   -2.11725
(kg/m^3)


10 bar, constraints= none
timestep 0.5 fs

Statistics over 51 steps [ 250. through 500. ps ], 2 data sets
All statistics are over 50001 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Temperature  299.92   0.114.86352  -0.139097  (K)
Density 600.689  214.759711.6485
(kg/m^3)


;Run control
integrator  =  md
dt  =  0.002 ; 0.0005 for constraints =none
otherwise blows up
nsteps  =  100
nstcomm =  100

;Output control
nstenergy   =  100
nstxout =  100
nstvout =  0
nstfout =  0
nstlog  =  1000
nstxtcout  =  1000

;Neighbor searching
nstlist =  10
ns_type =  grid

;Electrostatics/VdW
coulombtype =  shift
vdw-type=  Shift
rcoulomb-switch =  0
rvdw-switch =  0.9

;Cut-offs
rlist   =  1.25
rcoulomb=  1.0
rvdw=  1.0


;Temperature coupling
Tcoupl  =  v-rescale
tc-grps =  System
tau_t   =  0.1
ref_t   =  300

;Pressure coupling
Pcoupl  =  Parrinello-Rahman
Pcoupltype  =  isotropic
tau_p   =  2
compressibility =  4.5e-5 4.5e-5
ref_p   =  10

constraints = all-bonds
constraint-algorithm = lincs
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Error in energy group exclusion

[Justin A. Lemkul]

bipin singh wrote:

Hello users,
I am getting the following warning during the grompp
-
WARNING 1 [file md.mdp]:
  Can not exclude the lattice Coulomb energy between energy groups
---

I am providing the following energy groups and  energy exclusion group
in my mdp file
energygrps=Protein SOL
energygrp_excl=Protein Protein SOL SOL

Please suggest me, why I am getting the above error and how to get rid
of this error.



Presumably you're using PME for long-range electrostatics.  The message you're 
getting is grompp trying to help you realize that with PME it is not possible to 
completely exclude all energetic terms, since the long-range mesh is always 
calculated.  Only short-range nonbonded interactions (LJ and Coulombic terms) 
are excluded in the mechanism above.


-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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Error in energy group exclusion

[Peter C. Lai]

On 2011-05-23 10:54:20AM -0500, bipin singh wrote:
> Hello users,
> I am getting the following warning during the grompp
> -
> WARNING 1 [file md.mdp]:
>   Can not exclude the lattice Coulomb energy between energy groups
> ---
> 
> I am providing the following energy groups and  energy exclusion group
> in my mdp file
> energygrps=Protein SOL
> energygrp_excl=Protein Protein SOL SOL
> 
> Please suggest me, why I am getting the above error and how to get rid
> of this error.

Don't use PME? You cannot do electrostatic exclusions between groups under
the PME scheme.

See also
http://lists.gromacs.org/pipermail/gmx-users/2011-May/060993.html
-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: NPT for compressing

[Vitaly Chaban]

Incredible!


On Mon, May 23, 2011 at 11:40 AM, Elisabeth  wrote:
> Thanks for your hint. Employing a 0.5 fs timestep resolved the problem.
>
> On 20 May 2011 22:58, Vitaly Chaban  wrote:
>>
>> > When I use constraints for all-bonds and dt of 0.002 compressing the box
>> > works well and I get density of above 600 SI which is the actual density
>> > of
>> > alkane. Can any one help why setting no constraints and dt=0.001 leads
>> > to
>> > the error message shown above. When no constraints is used PR doesnt
>> > work
>> > for compressing and berendsen gives desired densty only for high
>> > pressures
>> > above 50 bar. I need to study my system at different pressures from 10
>> > bar... please comment on this.. Thanks.
>>
>>
>> Use smaller time-step while you are compressing the system. This
>> should eliminate the above problems.
>>
>> --
>> Dr. Vitaly V. Chaban, Department of Chemistry
>> University of Rochester, Rochester, New York 14627-0216
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Error in energy group exclusion

[bipin singh]

Hello users,
I am getting the following warning during the grompp
-
WARNING 1 [file md.mdp]:
  Can not exclude the lattice Coulomb energy between energy groups
---

I am providing the following energy groups and  energy exclusion group
in my mdp file
energygrps=Protein SOL
energygrp_excl=Protein Protein SOL SOL

Please suggest me, why I am getting the above error and how to get rid
of this error.


-- 
---
Regards,
Bipin Singh
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] -ci option

[Peter C. Lai]

On 2011-05-23 10:43:49AM -0500, shivangi nangia wrote:
> Dear gmx users,
> 
> I want to insert few ions in my system randomly.
> 
> -ci option does that, but I want various "different" random configurations of 
> the ions in my system.
> 
> Using -ci option does randomly place ions but at the same coordinates each 
> time.
> 
> Is there a way to randomly generate various configurations of ions each time 
> on using -ci?
> 
> 
> Thanks,
> SN
> 

Try using genion instead?
It allows for -seed to specify random factor.

-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] -ci option

[Justin A. Lemkul]

shivangi nangia wrote:

Dear gmx users,

I want to insert few ions in my system randomly.

-ci option does that, but I want various "different" random 
configurations of the ions in my system.


Using -ci option does randomly place ions but at the same coordinates 
each time.


Is there a way to randomly generate various configurations of ions each 
time on using -ci?




Set a different value of -seed.

-Justin



Thanks,
SN



--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] -ci option

[Jon Kapla]

On 2011-05-23 17:43, shivangi nangia wrote:

Dear gmx users,

I want to insert few ions in my system randomly.

-ci option does that, but I want various "different" random 
configurations of the ions in my system.


Using -ci option does randomly place ions but at the same coordinates 
each time.


Is there a way to randomly generate various configurations of ions 
each time on using -ci?



Thanks,
SN

If you're using genbox then I would guess that you can use the -seed 
option to set another random seed.


Regards
Jon

--
_

Jon Kapla
  Division of Physical Chemistry
  Dpt. of Materials and Environmental Chemistry (MMK)
  Arrhenius Laboratory
  Stockholm University
  SE-106 91 Stockholm
Pos:PhD Student
Phone:  +46 8 16 11 79 (office)
Phone:  +46 70 304 19 89 (cell)
E-mail: jon.ka...@mmk.su.se
_

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] -ci option

[shivangi nangia]

Dear gmx users,

I want to insert few ions in my system randomly.

-ci option does that, but I want various "different" random configurations
of the ions in my system.

Using -ci option does randomly place ions but at the same coordinates each
time.

Is there a way to randomly generate various configurations of ions each time
on using -ci?


Thanks,
SN
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Velocity and temperature profiles

[Mark Abraham]

On 23/05/2011 10:38 PM, Mikhail Stukan wrote:


Dear gmx-users,

I am currently working on a fluid flow in a nano-channel and would 
like to build  velocity and temperature profiles across the channel. 
Could anyone give me a hint if it is possible to do this using  the 
existing set of GROMACS tools?




Possible, but not easy. So long as you save simulation velocities in 
your trajectory file, you'd then have to do some tedious scripting of 
g_select to select suitable atoms for each point in your profile for 
each trajectory snapshot. Then for each selection from each snapshot 
you'd have to construct a matching topology to prepare a subset run 
input file to match with a subset of a trajectory frame to pass to mdrun 
-rerun to measure the local temperature of the subset.


This temperature might mean even less than a normal MD "temperature". 
See Eastwood, M. P., Stafford, K. A., Lippert, R. A., Jensen, M. O., 
Maragakis, P., Predescu, C., Dror, R. O., Shaw, D. E. Equipartition and 
the calculation of temperature in biomolecular simulations. J. Chem. 
Theory Comp. ASAP:DOI: 10.1021/ct9002916, 2010.


Mark
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Velocity and temperature profiles

[Mikhail Stukan]

Dear gmx-users,

I am currently working on a fluid flow in a nano-channel and would like to 
build  velocity and temperature profiles across the channel. Could anyone give 
me a hint if it is possible to do this using  the existing set of GROMACS tools?

Many thanks in advance,
Mikhail


=
Dr Mikhail Stukan
Schlumberger Dhahran Carbonate Research Center,
Dhahran Techno Valley  - KFUPM,
P.O. Box 39011, Dammam / Doha Camp  31942,
Kingdom of Saudi Arabia
Tel: +966 3 331 6182
Fax:+966 3 330 0845
mstu...@slb.com

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] memory problem of g_hbond?

[Mark Abraham]

On 23/05/2011 7:23 PM, Baofu Qiao wrote:


Thanks a lot, Erik!

But could you specify how to build the index of water in certain 
region, say 0

g_select can make such a selection, but you will have to script any 
approach using its output to build (say) a pseudo-trajectory of the 
water molecules that satisfy that criterion. However before you do that, 
surely the hydrogen bonding matrix would lose meaning if molecules were 
allow to diffuse out of the region treatrd by the matrix.


Mark





On 05/23/2011 11:05 AM, Erik Marklund wrote:

Baofu Qiao skrev 2011-05-23 10.47:

Hi all,

Very recently, I meet a problem when using g_hbond (gromacs 4.5.3 
with the bugfixed)

*
Select a group: Selected 1: 'SOL'
Select a group: Selected 1: 'SOL'
Calculating hydrogen bonds in SOL (98280 atoms)
Found 32760 donors and 32760 acceptors
*Segmentation fault*
*
I check the code of gmx_hbond.c. The problem comes from the function 
of "mk_hbmap". However, g_hbond doesn't complain  
"gmx_fatal(FARGS,"Could not allocate enough memory for hbmap")' 
while giving the "Segmentation fault". My first guess is 1) the 
function doesn't work correctly; 2) there is no enough memory for 
32760 donors and 32760 acceptors.


What I really want to calculate is the HB correlation function is 
some slab structure of thickness of about 3ns, where there is only 
~3000 waters. Can someone give me some suggestions? Thanks a lot!


best regards,
Baofu Qiao

That sounds like a memory problem indeed, and it could be outside the 
control of g_hbond. From the manpages of malloc:


"By default, Linux follows an  optimistic  memory  allocation  
strategy. This  means  that  when malloc() returns non-NULL there is 
no guarantee that the memory really is available. This is a really 
bad bug."


g_hbond checks for NULL pointers to decide whether snew() was 
successful or not. Hence the menetioned bug could be the culprit. 
That said, the hbmap of your system requires 32760^2 pointers (> 8 Gb 
on 64 bit systems) that in turn points to existence arrays with size 
that scales with trajectory length. Hence you will easily run out of 
memory. I suggest that you build the acf for a subset of your system, 
e.g. 1000 waters. The acf will converge slower, but have the same 
features. You can do this many times and take an average for better 
statistics.


Cheers,



--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] memory problem of g_hbond?

[Erik Marklund]

Hi,

Try g_select. I've never used it myself, so I can't say exactly what 
it's capable of. Or use a gro file to extract the molecules that are 
fulfil your criterion. ndx-files are just sets of atom indices in rather 
free ascii format, so making them from gro files with standard *nix 
tools is pretty simple.


Erik

Baofu Qiao skrev 2011-05-23 11.23:


Thanks a lot, Erik!

But could you specify how to build the index of water in certain 
region, say 0



On 05/23/2011 11:05 AM, Erik Marklund wrote:

Baofu Qiao skrev 2011-05-23 10.47:

Hi all,

Very recently, I meet a problem when using g_hbond (gromacs 4.5.3 
with the bugfixed)

*
Select a group: Selected 1: 'SOL'
Select a group: Selected 1: 'SOL'
Calculating hydrogen bonds in SOL (98280 atoms)
Found 32760 donors and 32760 acceptors
*Segmentation fault*
*
I check the code of gmx_hbond.c. The problem comes from the function 
of "mk_hbmap". However, g_hbond doesn't complain  
"gmx_fatal(FARGS,"Could not allocate enough memory for hbmap")' 
while giving the "Segmentation fault". My first guess is 1) the 
function doesn't work correctly; 2) there is no enough memory for 
32760 donors and 32760 acceptors.


What I really want to calculate is the HB correlation function is 
some slab structure of thickness of about 3ns, where there is only 
~3000 waters. Can someone give me some suggestions? Thanks a lot!


best regards,
Baofu Qiao

That sounds like a memory problem indeed, and it could be outside the 
control of g_hbond. From the manpages of malloc:


"By default, Linux follows an  optimistic  memory  allocation  
strategy. This  means  that  when malloc() returns non-NULL there is 
no guarantee that the memory really is available. This is a really 
bad bug."


g_hbond checks for NULL pointers to decide whether snew() was 
successful or not. Hence the menetioned bug could be the culprit. 
That said, the hbmap of your system requires 32760^2 pointers (> 8 Gb 
on 64 bit systems) that in turn points to existence arrays with size 
that scales with trajectory length. Hence you will easily run out of 
memory. I suggest that you build the acf for a subset of your system, 
e.g. 1000 waters. The acf will converge slower, but have the same 
features. You can do this many times and take an average for better 
statistics.


Cheers,




--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] memory problem of g_hbond?

[Baofu Qiao]

Thanks a lot, Erik!

But could you specify how to build the index of water in certain region, 
say 0



On 05/23/2011 11:05 AM, Erik Marklund wrote:

Baofu Qiao skrev 2011-05-23 10.47:

Hi all,

Very recently, I meet a problem when using g_hbond (gromacs 4.5.3 
with the bugfixed)

*
Select a group: Selected 1: 'SOL'
Select a group: Selected 1: 'SOL'
Calculating hydrogen bonds in SOL (98280 atoms)
Found 32760 donors and 32760 acceptors
*Segmentation fault*
*
I check the code of gmx_hbond.c. The problem comes from the function 
of "mk_hbmap". However, g_hbond doesn't complain  
"gmx_fatal(FARGS,"Could not allocate enough memory for hbmap")' while 
giving the "Segmentation fault". My first guess is 1) the function 
doesn't work correctly; 2) there is no enough memory for 32760 donors 
and 32760 acceptors.


What I really want to calculate is the HB correlation function is 
some slab structure of thickness of about 3ns, where there is only 
~3000 waters. Can someone give me some suggestions? Thanks a lot!


best regards,
Baofu Qiao

That sounds like a memory problem indeed, and it could be outside the 
control of g_hbond. From the manpages of malloc:


"By default, Linux follows an  optimistic  memory  allocation  
strategy. This  means  that  when malloc() returns non-NULL there is 
no guarantee that the memory really is available. This is a really bad 
bug."


g_hbond checks for NULL pointers to decide whether snew() was 
successful or not. Hence the menetioned bug could be the culprit. That 
said, the hbmap of your system requires 32760^2 pointers (> 8 Gb on 64 
bit systems) that in turn points to existence arrays with size that 
scales with trajectory length. Hence you will easily run out of 
memory. I suggest that you build the acf for a subset of your system, 
e.g. 1000 waters. The acf will converge slower, but have the same 
features. You can do this many times and take an average for better 
statistics.


Cheers,


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] need help

[Mark Abraham]

On 23/05/2011 6:57 PM, rashi parihar wrote:


Hi all
I have an ligand having NI atom(Nickel) .Now problem is this when I am 
running PRODRG server ,ligand topology can not be created and error is 
coming

*unsupported atom type NI (atom 'NI2 ') in your coordinates*.now how to 
overcome this problem? plz help me!!


See http://www.gromacs.org/Documentation/How-tos/Parameterization

Mark
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] memory problem of g_hbond?

[Erik Marklund]

Baofu Qiao skrev 2011-05-23 10.47:

Hi all,

Very recently, I meet a problem when using g_hbond (gromacs 4.5.3 with 
the bugfixed)

*
Select a group: Selected 1: 'SOL'
Select a group: Selected 1: 'SOL'
Calculating hydrogen bonds in SOL (98280 atoms)
Found 32760 donors and 32760 acceptors
*Segmentation fault*
*
I check the code of gmx_hbond.c. The problem comes from the function 
of "mk_hbmap". However, g_hbond doesn't complain  
"gmx_fatal(FARGS,"Could not allocate enough memory for hbmap")' while 
giving the "Segmentation fault". My first guess is 1) the function 
doesn't work correctly; 2) there is no enough memory for 32760 donors 
and 32760 acceptors.


What I really want to calculate is the HB correlation function is some 
slab structure of thickness of about 3ns, where there is only ~3000 
waters. Can someone give me some suggestions? Thanks a lot!


best regards,
Baofu Qiao

That sounds like a memory problem indeed, and it could be outside the 
control of g_hbond. From the manpages of malloc:


"By default, Linux follows an  optimistic  memory  allocation  strategy. 
This  means  that  when malloc() returns non-NULL there is no guarantee 
that the memory really is available. This is a really bad bug."


g_hbond checks for NULL pointers to decide whether snew() was successful 
or not. Hence the menetioned bug could be the culprit. That said, the 
hbmap of your system requires 32760^2 pointers (> 8 Gb on 64 bit 
systems) that in turn points to existence arrays with size that scales 
with trajectory length. Hence you will easily run out of memory. I 
suggest that you build the acf for a subset of your system, e.g. 1000 
waters. The acf will converge slower, but have the same features. You 
can do this many times and take an average for better statistics.


Cheers,

--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] need help

[rashi parihar]

Hi all
I have an ligand having NI atom(Nickel) .Now problem is this when I am
running PRODRG server ,ligand topology can not be created and error is
coming

*unsupported atom type NI (atom 'NI2 ') in your coordinates*.now how
to overcome this problem? plz help me!!

-- 

[image: images[12]]

“Many Smiles Begin Because Of Another Smile . . . ."

Regards,
Rashi
<>-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] memory problem of g_hbond?

[Baofu Qiao]

  
  
Hi all,

Very recently, I meet a problem when using g_hbond (gromacs 4.5.3
with the bugfixed)
*
Select a group: Selected 1: 'SOL'
Select a group: Selected 1: 'SOL'
Calculating hydrogen bonds in SOL (98280 atoms)
Found 32760 donors and 32760 acceptors
Segmentation fault
*
I check the code of gmx_hbond.c. The problem comes from the function
of "mk_hbmap". However, g_hbond doesn't complain 
"gmx_fatal(FARGS,"Could not allocate enough memory for hbmap")'
while giving the "Segmentation fault". My first guess is 1) the
function doesn't work correctly; 2) there is no enough memory for
32760 donors and 32760 acceptors.

What I really want to calculate is the HB correlation function is
some slab structure of thickness of about 3ns, where there is only
~3000 waters. Can someone give me some suggestions? Thanks a lot!

best regards,
Baofu Qiao

  

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists