[gmx-users] fatal error

[Gavin Melaugh]

Hi all

Why is pull geometry direction not supported in g_wham ? I got the
following error. I did this to compare with the same simulations but
with pull geometry = distance.

Fatal error:
Pull geometry direction not supported

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Re: [gmx-users] Why does the -append option exist?

[Sander Pronk]

Hi Dimitar,Thanks for the bug report. Would you mind trying the test program I attached on the same file system that you get the truncated files on? compile it with gcc testje.c -o testioSander

testje.c
Description: Binary data
On Jun 7, 2011, at 23:21 , Dimitar Pachov wrote:Hello,Just a quick update after a few shorts tests we (my colleague and I) quickly did. First, using "You can emulate this yourself by calling "sleep 10s" before mdrun and see if that's long enough to solve the latency issue in your case."
doesn't work for a few reasons, mainly because it doesn't seem to be a latency issue, but also because the load on a node is not affected by "sleep".However, you can reproduce the behavior I have observed pretty easily. It seems to be related to the values of the pointers to the *xtc, *trr, *edr, etc files written at the end of the checkpoint file after abrupt crashes AND to the frequency of access (opening) to those files. How to test:
 1. In your input *mdp file put a high frequency of saving coordinates to, say, the *xtc (10, for example) and a low frequency for the *trr file (10,000, for example).2. Run GROMACS (mdrun -s run.tpr -v -cpi -deffnm run)
3. Kill abruptly the run shortly after that (say, after 10-100 steps).4. You should have a few frames written in the *xtc file, and the only one (the first) in the *trr file. The *cpt file should have different from zero values for "file_offset_low" for all of these files (the pointers have been updated).
5. Restart GROMACS (mdrun -s run.tpr -v -cpi -deffnm run). 6. Kill abruptly the run shortly after that (say, after 10-100 steps). Pay attention that the frequency for accessing/writing the *trr has not been reached. 
7. You should have a few additional frames written in the *xtc file, while the *trr will still have only 1 frame (the first). The *cpt file now has updated all pointer values "file_offset_low", BUT the pointer to the *trr has acquired a value of 0. Obviously, we already now what will happen if we restart again from this last *cpt file. 
8. Restart GROMACS (mdrun -s run.tpr -v -cpi -deffnm run). 9. Kill it. 10. File *trr has size zero. Therefore, if a run is killed before the files are accessed for writing (depending on the chosen frequency), the file offset values reported in the *cpt file doesn't seem to be accordingly updated, and hence a new restart inevitably leads to overwritten output files.
 Do you think this is fixable?Thanks,DimitarOn Sun, Jun 5, 2011 at 6:20 PM, Roland Schulz  wrote:
Two comments about the discussion: 1) I agree that buffered output (Kernel buffers - not application buffers) should not affect I/O. If it does it should be filed as bug to the OS. Maybe someone can write a short test application which tries to reproduce this idea. Thus writing to a file from one node and immediate after one test program is killed on one node writing to it from some other node.


2) We lock files but only the log file. The idea is that we only need to guarantee that the set of files is only accessed by one application. This seems safe but in case someone sees a way of how the trajectory is opened without the log file being opened, please file a bug.


RolandOn Sun, Jun 5, 2011 at 10:13 AM, Mark Abraham  wrote:




  


  
  
On 5/06/2011 11:08 PM, Francesco Oteri wrote:

  
  
  Dear Dimitar, 
  I'm following the debate regarding:
  

  


  
  

  The point was not "why" I was getting
the restarts, but the fact itself that I was getting
restarts close in time, as I stated in my first post. I
actually also don't know whether jobs are deleted or
suspended. I've thought that a job returned back to the
queue will basically start from the beginning when later
moved to an empty slot ... so don't understand the
difference from that perspective.
  

  
  
  In the second mail yoo say:
  
  
Submitted by:

ii=1
ifmpi="mpirun -np $NSLOTS"

   if [ ! -f run${ii}-i.tpr ];then

        cp run${ii}.tpr run${ii}-i.tpr 
        tpbconv -s run${ii}-i.tpr -until
  20 -o run${ii}.tpr 
     fi
  

     k=`ls md-${ii}*.out | wc -l`
     outfile="md-${ii}-$k.out"
     if [[ -f run${ii}.cpt ]]; then
     
         $ifmpi `which mdrun` -s
  run${ii}.tpr -cpi run${ii}.cpt -v -deffnm run${ii} -npme 0
  > $outfile  2>&1  
  

     fi

=
  
  
  If I understand well, you are submitting the SERIAL  mdrun.
  This means that multiple instances of mdrun are running at the
  same time.
  

Re: [gmx-users] Essential dynamics - concepts

[Tsjerk Wassenaar]

Hi Kavya,

> Thanks sir. I will go through them. However I have referred -
> "A Tutorial on Principle component Analysis" by  Lindsay I Smith.
> Which gave a good understanding about the concepts. Still I
> have some doubts regarding eigen values, as you have told
> I will think over them again.

I know that one :) I'd advise others thinking of using PCA in MD to
also read it...  It also pays off to read a few more, though, to get
slightly different viewing angles and to get used to different ways of
telling the same story.

> But one statement I was not clear from your previous mail  that -
> "An eigenvalue is an RMSF of the collective motion."

I shouldn't have said RMSF, as it's not the root. The first eigenvalue
is the variance or mean square fluctuation of the projection of your
data onto the first eigenvector.

>
> These eigenvalues are the solutions for an Nth order equation
> arising from N X N covar (sorry for using this term again) matrix
> (considering only x component). If we consider this covar matrix
> as a transformation matrix, eigen value would give the magnitude
> and direction by which the eigenvector is transformed linearly.
> Is it correct?

No, the matrix of eigenvectors is a transformation (rotation) matrix.
The eigenvectors in a sense give the directions of motion, and the
eigenvalues the magnitudes.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] Gromacs-4.5.4 install error

[xuji]

Hi all gmx-users:

I install gromacs-4.5.4, with

tar xzf gromacs-4.5.4.tar.gz
cd gromacs-4.5.4
export MPICC=/usr/mpi/gcc/mvapich2-1.4.1/bin/mpicc 
./configure --prefix=/home/xuji/bin/gmx_4.5.4/parallel_float --enable-mpi 
--program-suffix=_mpi --without-x --with-fft=fftw3 --enable-all-static 
--without-xml --with-pic CPPFLAGS=-I/home/xuji/bin/fftw3_f/include/ 
LDFLAGS=-L/home/xuji/bin/fftw3_f/lib/ 
make -j 8

but always got following errors:

Making all in kernel
make[3]: Entering directory `/home/xuji/src/gromacs-4.5.4/src/kernel'
/bin/sh ../../libtool --tag=CC   --mode=link 
/usr/mpi/gcc/mvapich2-1.4.1/bin/mpicc  -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99  
-L/home/xuji/bin/fftw3_f/lib/   -all-static -o grompp grompp.o 
libgmxpreprocess_mpi.la  ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la  -lnsl 
-lm  
/usr/mpi/gcc/mvapich2-1.4.1/bin/mpicc -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 
-static -o grompp grompp.o  -L/home/xuji/bin/fftw3_f/lib/ 
./.libs/libgmxpreprocess_mpi.a 
/home/xuji/src/gromacs-4.5.4/src/mdlib/.libs/libmd_mpi.a 
../mdlib/.libs/libmd_mpi.a /home/xuji/bin/fftw3_f/lib/libfftw3f.a 
/home/xuji/src/gromacs-4.5.4/src/gmxlib/.libs/libgmx_mpi.a 
../gmxlib/.libs/libgmx_mpi.a -lnsl -lm  
/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(simple_pmi.o): In function 
`PMI_Init':
(.text+0x1690): warning: Using 'gethostbyname' in statically linked 
applications requires at runtime the shared libraries from the glibc version 
used for linking
/usr/lib64/libc.a(malloc.o): In function `__malloc_check_init':
(.text+0x13d0): multiple definition of `__malloc_check_init'
/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x8c0): 
first defined here
/usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed from 113 in 
/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o) to 107 in 
/usr/lib64/libc.a(malloc.o)
/usr/lib64/libc.a(malloc.o): In function `free':
(.text+0x6da0): multiple definition of `free'
/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x3260): 
first defined here
/usr/bin/ld: Warning: size of symbol `free' changed from 247 in 
/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o) to 375 in 
/usr/lib64/libc.a(malloc.o)
/usr/lib64/libc.a(malloc.o): In function `malloc':
(.text+0x55b0): multiple definition of `malloc'
/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x3370): 
first defined here
/usr/bin/ld: Warning: size of symbol `malloc' changed from 364 in 
/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o) to 547 in 
/usr/lib64/libc.a(malloc.o)
/usr/lib64/libc.a(malloc.o): In function `realloc':
(.text+0x6f20): multiple definition of `realloc'
/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x3740): 
first defined here
/usr/bin/ld: Warning: size of symbol `realloc' changed from 508 in 
/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o) to 1123 in 
/usr/lib64/libc.a(malloc.o)
/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mem_hooks.o): In function 
`set_real_munmap_ptr':
(.text+0x1e): undefined reference to `dlsym'
/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mem_hooks.o): In function 
`set_real_munmap_ptr':
(.text+0x26): undefined reference to `dlerror'
/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mem_hooks.o): In function 
`mvapich2_minit':
(.text+0x14c): undefined reference to `dlerror'
/usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function `load_driver':
(.text+0xc7): undefined reference to `dlopen'
/usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function `load_driver':
(.text+0x102): undefined reference to `dlerror'
/usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function `ibverbs_init':
(.text+0x11af): undefined reference to `dlopen'
/usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function `ibverbs_init':
(.text+0x11c0): undefined reference to `dlclose'
/usr/lib64/libibverbs.a(src_libibverbs_la-verbs.o): In function 
`ibv_create_comp_channel':
(.text+0xb76): undefined reference to `pthread_mutex_trylock'
collect2: ld returned 1 exit status
make[3]: *** [grompp] Error 1
make[3]: Leaving directory `/home/xuji/src/gromacs-4.5.4/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/xuji/src/gromacs-4.5.4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/xuji/src/gromacs-4.5.4/src'
make: *** [all-recursive] Error 1


Can someone show me what's wrong?
Appreciate any help in advance!


2011-06-08 




Best 
wishes！

Ji Xu
The State Key Laboratory of Multiphase Complex System
Institute of Process Engineering
Chinese Academy of Sciences
Beijing 100190, China
Tel.: +86 10 8262 3713-804 
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[gmx-users] effect of slab geometry correction on Coulomb energies for interface systems

[Ozge Engin]

Hi all,

I am trying to investigate how the slab geometry correction affects
calculated Coulomb energies for interface systems. I have an air/water
interface with a box size of 3x3x9 nm. I ran 2 independent simulations with
changing ewald_geometry option: 3d (default value), and 3dc. You can find
short and reciprocal Coulomb  energies below:

  *3d 3dc *
short-range Coulomb -45260.2 (6.5)   -45258.4 (5)
Reciprocal Coulomb  -3325.72 (0.13) -3325.54 (0.1)

I am wondering why short-range and reciprocal Coulomb energies are the same
within the error bars even though I use different schemes for
ewald_geometry?

Regards

-- 

Ozge Engin- PhD candidate
Koc University, College of Engineering
Dept. of Computational Sciences & Engineering
Rumelifeneri Yolu, 34450 Sariyer/Istanbul, Turkey
Email: ozge.en...@gmail.com, ozen...@ku.edu.tr
Phone:+90-212-338-1542
Fax:  +90-212-338-1548
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Re: [gmx-users] reg linear interpolation

[Justin A. Lemkul]

vidhya sankar wrote:

Dear justin,
 Thank you for your previous reply.
Can i use g_morph  tool in gromacs for wild type and mutated Pdb
Because it ask two input PDB files
should these two files contains equal no residues? otherwise can i use 
different PDB (WT and Mutated PDB )  which differ only by two or more 
residue due to mutation




Try it and see.  I doubt it will work if the number of atoms is dissimilar. 
Also take note of the second sentence in the help description.


-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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[gmx-users] distance/direction PMF

[Gavin Melaugh]

Hi all

Could someone please get back to me on this. I have ran two sets of
umbrella sampling simulations
1- Using pull_geometry = distance, and pull_dim = Y Y Y
2- Using pull_geometry = direction, with pull_vec = 0.462808 0.494125
0.735968
 
In both cases I wish to calculate the PMF for taking a host out of a
guest. I specify the distance between the COM of the two groups in the
respective mdp files. The two curves I get are completely different
which has leads me to ask a couple of questions:

1) Does the vector change as the dynamics evolves (i.e is it just
relative between the two points) or does it remain fixed in space?

2) Using umbrella sampling in the second case does the relative position
of the pull group (guest) fluctuate about the distance along the
specified vector?

Note- I couldn't run g_wham with pull_geometry = direction in my current
version of gromacs, so I ran it in 4.5.3 but I had to use the -if
pullf-files.xvg option.

Some help would be appreciated as I have to be sure of what the program
is actually doing.

Many thanks

Gavin
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[gmx-users] problem in g_density

[cdalgicdir]

Hi,

The simulation box consists of layers of cyclohexane and vacuum. 
Ensemble is NVT.


The density profiles of cyclohexane for 5-10 ns, 10-15 ns and 15-20 ns 
coincide. However the density profile for 5-20 ns is significantly 
higher than the ones calculated.

g_density -n -b 5000 -e 2

If I calculate the 5-20 ns interval using every 5th frame the density 
profile resembles that of the 5-10, 10-15, 15-20 ns's.

g_density -n -b 5000 -e 2 -dt 5

Attached is the graph of these profiles.

I have tried this in 4.07, 4.5.3 and 4.5.4. The results are similar for 
all these versions.


I am aware that such inconsistencies may occur with g_density in NPT 
ensembles. However I am using a NVT ensemble. Is there something am I 
missing? And more importantly,  how should I decide which one is the 
correct density?


Thanks,
Cahit
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Re: [gmx-users] problem in g_density

[Mark Abraham]

On 8/06/2011 9:41 PM, cdalgicdir wrote:

Hi,

The simulation box consists of layers of cyclohexane and vacuum. 
Ensemble is NVT.


The density profiles of cyclohexane for 5-10 ns, 10-15 ns and 15-20 ns 
coincide. However the density profile for 5-20 ns is significantly 
higher than the ones calculated.

g_density -n -b 5000 -e 2

If I calculate the 5-20 ns interval using every 5th frame the density 
profile resembles that of the 5-10, 10-15, 15-20 ns's.

g_density -n -b 5000 -e 2 -dt 5

Attached is the graph of these profiles.

I have tried this in 4.07, 4.5.3 and 4.5.4. The results are similar 
for all these versions.


I am aware that such inconsistencies may occur with g_density in NPT 
ensembles. However I am using a NVT ensemble. Is there something am I 
missing? And more importantly,  how should I decide which one is the 
correct density?


I'd guess this is an artefact of the fact that the times in the 
trajectory file are not exactly multiples of the time step. That is just 
life - see 
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic. If so, 
one or more of these ranges is probably not computing over the set of 
frames you think it is. Consider using suitable non-integers for -b and 
-e, and avoiding -dt unless you know it will work on the times that 
exist. trjcat -settime can help, also.


Mark
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[gmx-users] Re: distance/direction PMF

[Justin A. Lemkul]

Gavin Melaugh wrote:

Hi all

Could someone please get back to me on this. I have ran two sets of
umbrella sampling simulations
1- Using pull_geometry = distance, and pull_dim = Y Y Y
2- Using pull_geometry = direction, with pull_vec = 0.462808 0.494125
0.735968
 
In both cases I wish to calculate the PMF for taking a host out of a

guest. I specify the distance between the COM of the two groups in the
respective mdp files. The two curves I get are completely different
which has leads me to ask a couple of questions:



You're doing two different things here, so I'd suspect that you're going to get 
a different answer with different settings.



1) Does the vector change as the dynamics evolves (i.e is it just
relative between the two points) or does it remain fixed in space?



It is relative.


2) Using umbrella sampling in the second case does the relative position
of the pull group (guest) fluctuate about the distance along the
specified vector?



Yes.


Note- I couldn't run g_wham with pull_geometry = direction in my current
version of gromacs, so I ran it in 4.5.3 but I had to use the -if
pullf-files.xvg option.



We'll have to assume that your "current version" is something in the 4.0.x 
series, so this outcome is expected.


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


Some help would be appreciated as I have to be sure of what the program
is actually doing.



There's always the code :)

-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] oplsaa vs. charmm

[Thomas Evangelidis]

Dear Prof van der Spoel and GROMACS users,

I have read the article "Scrutinizing Molecular Mechanics Force Fields..."
where it is demonstrated that AMBER99sb yields protein conformations that
are in better agreement with residual dipolar coupling, J-coupling and NOE
data, compared with other force fields. However, both proteins used for this
benchmark study (ubiquitin and protein G) are rather rigid, so I was
wondering if there is a similar analysis for flexible proteins/peptides. I
want to simulate a few intrinsically disordered proteins/peptides of length
between 40 and 100 aa and would like to know what would be the best choice
of force field to use. Any experience or knowledge on this matter would be
greatly appreciated!

thanks in advance,
Thomas



On 27 May 2011 19:01, David van der Spoel  wrote:

> On 2011-05-27 17.50, simon sham wrote:
>
>> Hi,
>> I have recently done two simulations on a protein at high temperature
>> near its melting temperature. At the beginning I used CHARMM forcefield,
>> and then OPLSAA to double check the results. There are some differences
>> in the structures between the forcefield used. I know different
>> forcefields can give different results. All parameters in the
>> simulations were the same except the forcefield. Is there anyway I can
>> tell which forcefield gives more reliable results?
>>
>> Thanks for the insights,
>>
>> Simon
>>
>>  You might want to check
>
> Oliver Lange, David van der Spoel and Bert de Groot: Scrutinizing Molecular
> Mechanics Force Fields on the Microsecond Timescale With NMR Data Biophys.
> J. 99 pp. 647-655 (2010)
>
> where we compare a number of FFs to NMR data.
>
> --
> 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
>
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>



-- 

==

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tev...@bioacademy.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [gmx-users] Re: distance/direction PMF

[Gavin Melaugh]

Hi Justin

Many thanks for the reply I know technically I am doing two different
things. However due to my starting conifgurations in both cases I would
expect similar results.
Could you confirm the following points

1) In pull_geometry=distance, and pull_dim =YYY; is the absolute
distance between the COM of both groups in all directions considered ?

2) In pull_geometry = direction, with a specified vector; I assume that
it is the distance between the two groups along this vector that is
considered?

3) Is the specified vector taken to be the vector connecting the two
points? Therefore are the desired distances in the mdp files essentially
the magnitudes of this vector at each window.

Cheers

Gavin


Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi all
>>
>> Could someone please get back to me on this. I have ran two sets of
>> umbrella sampling simulations
>> 1- Using pull_geometry = distance, and pull_dim = Y Y Y
>> 2- Using pull_geometry = direction, with pull_vec = 0.462808 0.494125
>> 0.735968
>>  
>> In both cases I wish to calculate the PMF for taking a host out of a
>> guest. I specify the distance between the COM of the two groups in the
>> respective mdp files. The two curves I get are completely different
>> which has leads me to ask a couple of questions:
>>
>
> You're doing two different things here, so I'd suspect that you're
> going to get a different answer with different settings.
>
>> 1) Does the vector change as the dynamics evolves (i.e is it just
>> relative between the two points) or does it remain fixed in space?
>>
>
> It is relative.
>
>> 2) Using umbrella sampling in the second case does the relative position
>> of the pull group (guest) fluctuate about the distance along the
>> specified vector?
>>
>
> Yes.
>
>> Note- I couldn't run g_wham with pull_geometry = direction in my current
>> version of gromacs, so I ran it in 4.5.3 but I had to use the -if
>> pullf-files.xvg option.
>>
>
> We'll have to assume that your "current version" is something in the
> 4.0.x series, so this outcome is expected.
>
> http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force
>
>> Some help would be appreciated as I have to be sure of what the program
>> is actually doing.
>>
>
> There's always the code :)
>
> -Justin
>

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Re: [gmx-users] Re: distance/direction PMF

[Justin A. Lemkul]

Gavin Melaugh wrote:

Hi Justin

Many thanks for the reply I know technically I am doing two different
things. However due to my starting conifgurations in both cases I would
expect similar results.
Could you confirm the following points

1) In pull_geometry=distance, and pull_dim =YYY; is the absolute
distance between the COM of both groups in all directions considered ?



Yes.


2) In pull_geometry = direction, with a specified vector; I assume that
it is the distance between the two groups along this vector that is
considered?



Should be.  Compare the output of g_dist with what grompp reports as the initial 
distance.



3) Is the specified vector taken to be the vector connecting the two
points? Therefore are the desired distances in the mdp files essentially
the magnitudes of this vector at each window.



Per the documentation, grompp normalizes the vector, so no, not directly.  But 
if you have proper settings for pull_init/pull_start, then the reference 
distance should be correctly calculated along the specified vector for each window.


-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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[gmx-users] g_hbond/g_sas - how is it calculated?

[Marzinek, Jan]

Hi,



I have a question related to the calculation of hydrogen bonds in Gromacs. As I 
read in Manual it comes from the distance between donor and acceptor ( <= 0.35 
nm) and the angle <=30 degr beween hydrogen and acceptor. The question is - why 
30 degr? How is it related to the reality?



The second thing is the claculation of the accessible surface area (g_sas) of 
the molecule for instance? It is not explained in manual and I am really 
curious how g_sas makes these calculations.

As my supervisors do not know the gromacs their questions are always about such 
details :)

However, I think it is really important to understand what you are really doing 
using commands in Gromacs which provide you with really detailed results.



Thank you in advance,



Jan


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Re: [gmx-users] g_hbond/g_sas - how is it calculated?

[lina]

On Wed, Jun 8, 2011 at 10:20 PM, Marzinek, Jan
 wrote:
> Hi,
>
>
>
> I have a question related to the calculation of hydrogen bonds in Gromacs.
> As I read in Manual it comes from the distance between donor and acceptor (
> <= 0.35 nm) and the angle <=30 degr beween hydrogen and acceptor. The
> question is - why 30 degr? How is it related to the reality?

It's a default value, you can change it when you need.

>
>
>
> The second thing is the claculation of the accessible surface area
> (g_sas) of the molecule for instance? It is not explained in manual and I am
> really curious how g_sas makes these calculations.
>
> As my supervisors do not know the gromacs their questions are always about
> such details :)
>
> However, I think it is really important to understand what you are really
> doing using commands in Gromacs which provide you with really detailed
> results.

All I can say is that, practice and problems are a good teacher.

>
>
>
> Thank you in advance,
>
>
>
> Jan
>
>
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lina
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Re: [gmx-users] g_hbond/g_sas - how is it calculated?

[Justin A. Lemkul]

Marzinek, Jan wrote:

Hi,

 

I have a question related to the calculation of hydrogen bonds in 
Gromacs. As I read in Manual it comes from the distance between donor 
and acceptor ( <= 0.35 nm) and the angle <=30 degr beween hydrogen and 
acceptor. The question is - why 30 degr? How is it related to the reality?


 


Hydrogen bond strength decreases with distance between the donor and acceptor 
and with deviation from linearity.  A survey of crystallographic structures 
shows that these are generally accepted criteria.  There is literature on this 
that dates back many decades.




The second thing is the claculation of the accessible surface area 
(g_sas) of the molecule for instance? It is not explained in manual and 
I am really curious how g_sas makes these calculations.




I'd suggest you look at the citation provided in the "PLEASE READ AND CITE THE 
FOLLOWING REFERENCE" section printed when running g_sas :)


-Justin

As my supervisors do not know the gromacs their questions are always 
about such details :)


However, I think it is really important to understand what you are 
really doing using commands in Gromacs which provide you with really 
detailed results.


 


Thank you in advance,

 


Jan

 



--


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] Re: distance/direction PMF

[Gavin Melaugh]

Justin

I did a short test on a particular window with the specified vector with
pull_init =0.78nm. I then grompp(ed) the final configuration and it gave
me a distance of 0.78 as the initial ditsance, fair enough. However when
I viewed the final line from g_dist the absolute distance or modulus was
0.815 nm, which agreed with the distance I calculated using a molecular
configuration editor. My question is therefore this, when using
pull_geometry =direction with a specified vector, How should one
interpret the initial distance provided by grompp? and how does Gromacs
deal with the fact that the vector between the two point changes during
the run ?

Cheers

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> Many thanks for the reply I know technically I am doing two different
>> things. However due to my starting conifgurations in both cases I would
>> expect similar results.
>> Could you confirm the following points
>>
>> 1) In pull_geometry=distance, and pull_dim =YYY; is the absolute
>> distance between the COM of both groups in all directions considered ?
>>
>
> Yes.
>
>> 2) In pull_geometry = direction, with a specified vector; I assume that
>> it is the distance between the two groups along this vector that is
>> considered?
>>
>
> Should be.  Compare the output of g_dist with what grompp reports as
> the initial distance.
>
>> 3) Is the specified vector taken to be the vector connecting the two
>> points? Therefore are the desired distances in the mdp files essentially
>> the magnitudes of this vector at each window.
>>
>
> Per the documentation, grompp normalizes the vector, so no, not
> directly.  But if you have proper settings for pull_init/pull_start,
> then the reference distance should be correctly calculated along the
> specified vector for each window.
>
> -Justin
>

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Re: [gmx-users] Re: distance/direction PMF

[Justin A. Lemkul]

Gavin Melaugh wrote:

Justin

I did a short test on a particular window with the specified vector with
pull_init =0.78nm. I then grompp(ed) the final configuration and it gave
me a distance of 0.78 as the initial ditsance, fair enough. However when
I viewed the final line from g_dist the absolute distance or modulus was
0.815 nm, which agreed with the distance I calculated using a molecular
configuration editor. My question is therefore this, when using
pull_geometry =direction with a specified vector, How should one
interpret the initial distance provided by grompp? and how does Gromacs
deal with the fact that the vector between the two point changes during
the run ?



You're telling grompp that the initial distance is 0.78 nm, so it's spitting 
that back out.  If that's not the true distance, then specify the correct 
quantity :)  The distance should be correctly detected with:


pull_start = yes
pull_init = 0

As for the second question, the vector doesn't change over the simulation, but 
the position of pull_group1 along that vector will.  That's what the umbrella 
potential is doing - it allows for harmonic oscillation along any of the 
dimensions specified by pull_vec/pull_dim (depending on the settings).


-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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[gmx-users] (no subject)

[Sven Benson]

Hello everybody,
I was wondering if the gro file format somehow supports 
systems that are greater than 9 molecules (not atoms), 
since the first column is fixed to size 5.


Anybody know a way around this problem? I've tried working 
with pdb, but GROMACS seems to ignore all entries with 
atom numbers larger than 9 atoms in this format as 
well.


Anybody know a way around this problem? I'd appreciate any 
helpful pointers.


Cheers
Sven
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Re: [gmx-users] (no subject)

[Justin A. Lemkul]

Sven Benson wrote:

Hello everybody,
I was wondering if the gro file format somehow supports systems that are 
greater than 9 molecules (not atoms), since the first column is 
fixed to size 5.


Anybody know a way around this problem? I've tried working with pdb, but 
GROMACS seems to ignore all entries with atom numbers larger than 9 
atoms in this format as well.




What command is ignoring atoms?  I've never had problems with systems >99,999 
atoms.  At 100,000 the numbers start over from zero, but you can still make 
index files that will then contain proper atom numbers (100,000 and beyond).


-Justin

Anybody know a way around this problem? I'd appreciate any helpful 
pointers.


Cheers
Sven


--


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] Re: distance/direction PMF

[Gavin Melaugh]

Hi Justin

Sorry maybe I was unclear before with my first point; the specified
distance in the mdp file is 0.78nm, which grompp returns back as the ref
distance. The "distance at the start" that grompp returns is also
0.78nm, even though the actual distance is 0.815nm. That's why I was
asking what this distance actually means, as it is not the absolute
distance between the reference groups.
Also as regards to your second point; what if in the initial
configurations the two reference groups do not lie along the stated vector?

Cheers

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Justin
>>
>> I did a short test on a particular window with the specified vector with
>> pull_init =0.78nm. I then grompp(ed) the final configuration and it gave
>> me a distance of 0.78 as the initial ditsance, fair enough. However when
>> I viewed the final line from g_dist the absolute distance or modulus was
>> 0.815 nm, which agreed with the distance I calculated using a molecular
>> configuration editor. My question is therefore this, when using
>> pull_geometry =direction with a specified vector, How should one
>> interpret the initial distance provided by grompp? and how does Gromacs
>> deal with the fact that the vector between the two point changes during
>> the run ?
>>
>
> You're telling grompp that the initial distance is 0.78 nm, so it's
> spitting that back out.  If that's not the true distance, then specify
> the correct quantity :)  The distance should be correctly detected with:
>
> pull_start = yes
> pull_init = 0
>
> As for the second question, the vector doesn't change over the
> simulation, but the position of pull_group1 along that vector will. 
> That's what the umbrella potential is doing - it allows for harmonic
> oscillation along any of the dimensions specified by pull_vec/pull_dim
> (depending on the settings).
>
> -Justin
>

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[gmx-users] Question about umbrella sampling "pull-geometry" option

[WU Yanbin]

Dear GMXers,

I'm running umbrella PMF calculations using GROMACS 4.5. A molecule is
placed at various locations of a channel to compute the energy barrier of
the entrance.

Below is the PMF section of mdp input, to compute the PMF around the
position of (4.04700, 4.0582, -2.2058). The pulling molecule is initially
placed close to the (4.04700, 4.0582, -2.2058) position.
The box size is 8.094*8.1164*6.0. The series of positions I considered is in
the z-coordinate range of -2.2 to -0.8.

---
pull= umbrella
pull_geometry   = position
pull_dim= N N Y
pull_start  = no
pull_ngroups= 1
pull_group0 =
pull_group1 = MOL1
pull_init1  = 4.04700  4.05820   -2.2058
pull_rate1  = 0.00
pull_k1 = 1000
pull_nstxout= 1000
pull_nstfout= 1000
---

For this particular configuration, should I use "pull-geometry=position" or
"pull-geometry=distance"? Or they are the same for this case?
I read the manual and PMF tutorial but cannot figure this out. Could anyone
provide more details about this?

Thank you.

Best,
Yanbin
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[gmx-users] a question about position restraint time for long alkyl chain molecules

[XUEMING TANG]

Hi there

I put a SDS Spherical micelle in solution and want to apply position
restraint before mdrun. Here I have a question: For macromolecules like
micelles, should the position restraint apply to not only the water
molecules (and ions) but also to the surfactant molecules in the micelle? If
it is also for the surfactant molecules, how to calculate the position
restraint time in this case.

Thank you and have a nice day!

Best!
Xueming
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Re: [gmx-users] Re: distance/direction PMF

[Justin A. Lemkul]

Gavin Melaugh wrote:

Hi Justin

Sorry maybe I was unclear before with my first point; the specified
distance in the mdp file is 0.78nm, which grompp returns back as the ref
distance. The "distance at the start" that grompp returns is also
0.78nm, even though the actual distance is 0.815nm. That's why I was
asking what this distance actually means, as it is not the absolute
distance between the reference groups.


As I said before, you're telling grompp to make that the reference distance. 
You say "the specified distance in the mdp file is 0.78 nm," therefore grompp is 
doing what it's told.  If that's not the desired distance, then don't set it as 
such.  Have you tried the combination I suggested in the last message?  Does it 
give an initial distance of 0.815 nm?



Also as regards to your second point; what if in the initial
configurations the two reference groups do not lie along the stated vector?



Hard to say, but probably you'll get some very high forces at the outset of the 
simulation as the simulation as the umbrella potential tries to force the pulled 
group to conform to the restraint specifications.  Whether or not that 
negatively impacts the ultimate result of the simulation is also an important 
consideration.  If you're pulling along a given vector, you should start with 
your reference coordinates as close to the desired location as possible.


-Justin


Cheers

Gavin

Justin A. Lemkul wrote:


Gavin Melaugh wrote:

Justin

I did a short test on a particular window with the specified vector with
pull_init =0.78nm. I then grompp(ed) the final configuration and it gave
me a distance of 0.78 as the initial ditsance, fair enough. However when
I viewed the final line from g_dist the absolute distance or modulus was
0.815 nm, which agreed with the distance I calculated using a molecular
configuration editor. My question is therefore this, when using
pull_geometry =direction with a specified vector, How should one
interpret the initial distance provided by grompp? and how does Gromacs
deal with the fact that the vector between the two point changes during
the run ?


You're telling grompp that the initial distance is 0.78 nm, so it's
spitting that back out.  If that's not the true distance, then specify
the correct quantity :)  The distance should be correctly detected with:

pull_start = yes
pull_init = 0

As for the second question, the vector doesn't change over the
simulation, but the position of pull_group1 along that vector will. 
That's what the umbrella potential is doing - it allows for harmonic

oscillation along any of the dimensions specified by pull_vec/pull_dim
(depending on the settings).

-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] Question about umbrella sampling "pull-geometry" option

[Justin A. Lemkul]

WU Yanbin wrote:

Dear GMXers,

I'm running umbrella PMF calculations using GROMACS 4.5. A molecule is 
placed at various locations of a channel to compute the energy barrier 
of the entrance.


Below is the PMF section of mdp input, to compute the PMF around the 
position of (4.04700, 4.0582, -2.2058). The pulling molecule is 
initially placed close to the (4.04700, 4.0582, -2.2058) position.
The box size is 8.094*8.1164*6.0. The series of positions I considered 
is in the z-coordinate range of -2.2 to -0.8.


---
pull= umbrella
pull_geometry   = position
pull_dim= N N Y
pull_start  = no  
pull_ngroups= 1

pull_group0 =
pull_group1 = MOL1
pull_init1  = 4.04700  4.05820   -2.2058
pull_rate1  = 0.00  
pull_k1 = 1000  
pull_nstxout= 1000

pull_nstfout= 1000
---

For this particular configuration, should I use "pull-geometry=position" 
or "pull-geometry=distance"? Or they are the same for this case?
I read the manual and PMF tutorial but cannot figure this out. Could 
anyone provide more details about this?




The "distance" method won't work.  Have you seen the following:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html

To pull something through a channel, either "position" or "direction" should be 
able to do it.


-Justin


Thank you.

Best,
Yanbin



--


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] a question about position restraint time for long alkyl chain molecules

[Justin A. Lemkul]

XUEMING TANG wrote:

Hi there

I put a SDS Spherical micelle in solution and want to apply position 
restraint before mdrun. Here I have a question: For macromolecules like 
micelles, should the position restraint apply to not only the water 
molecules (and ions) but also to the surfactant molecules in the 
micelle? If it is also for the surfactant molecules, how to calculate 
the position restraint time in this case. 



Why would you restrain the solvent?  That basically prevents equilibration from 
happening.  Then, if you restrain the solvent and surfactant, you truly 
accomplish nothing.


Likely the best course of action is to restrain the surfactant molecules, while 
allowing everything else to move freely.  Then, remove all restraints and 
equilibrate a while longer.


-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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[gmx-users] Calculation of unsaturated deuterium order parameters for POPC

[Thomas Piggot]

Hi Everyone,

I am facing a problem when calculating the lipid deuterium order 
parameters for the unsaturated carbons of the sn-2 tail of POPC using 
g_order with GROMACS version 4.5.4 (although I have tried other older 
versions too but they all give the same results).


Firstly, I should say the the calculation of the order parameters for 
the saturated sn-1 chain (and also both chains of DPPC) behave as I 
would expect, and produce order parameters that compare well to 
previously published simulations and experimental values.


To calculate the order parameters of the unsaturated chain I am 
following the approach as given on the GROMACS website 
(http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order), so 
splitting the calculation into two parts for the saturated and 
unsaturated regions of the chain. The problem I am facing is that the 
order parameter for carbon 9 (so the first carbon in the double bond), 
calculated using the -unsat option, is much larger than expected. By 
this I mean that for the two different force fields I have tested 
(namely the CHARMM36 parameters of Klauda et al., and the GROMOS 53A6L 
parameters of Poger et al.) the order parameter for this carbon is much 
larger than the published simulation values and also much larger than 
experimental values. To highlight this, I have just put the numbers I 
have obtained using g_order for this carbon below, and compared to some 
rough values I have estimated from figures provided in the Klauda and 
Poger papers:


CHARMM36

g_order:0.133732
Klauda estimate:0.06


GROMOS53A6L:

g_order:0.199651
Poger estimate: 0.07

Myself and a colleague have tried looking into the code to determine how 
the order parameters are calculated using the -unsat option, however we 
couldn't quite follow the calculation. Hopefully someone who knows 
something more about g_order can help with this problem. Again I should 
stress that it appears that the main difference in order parameters 
between what I have calculated and the published ones is just in this 
one carbon, for both force fields. A similar issue to this has also been 
reported previously on the list for this carbon of POPC using the 
'Berger' force field 
(http://lists.gromacs.org/pipermail/gmx-users/2010-February/049072.html).


Thank you for any help anyone can give

Cheers

Tom

--
Dr Thomas Piggot
University of Southampton, UK.
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Re: [gmx-users] Re: distance/direction PMF

[Gavin Melaugh]

Yeah

 I set pull_init =0, and pull_start = yes, and it still gave a "distance
at start" as 0.78nm. It must be doing something funny because with
pull_vec, because when I use pull_geometry = distance and pull_dim
= Y Y Y, the distance 0.815nm is returned as the "distance at start",
which is the actual distance between the two groups.

Cheers

Gavin
 
Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> Sorry maybe I was unclear before with my first point; the specified
>> distance in the mdp file is 0.78nm, which grompp returns back as the ref
>> distance. The "distance at the start" that grompp returns is also
>> 0.78nm, even though the actual distance is 0.815nm. That's why I was
>> asking what this distance actually means, as it is not the absolute
>> distance between the reference groups.
>
> As I said before, you're telling grompp to make that the reference
> distance. You say "the specified distance in the mdp file is 0.78 nm,"
> therefore grompp is doing what it's told.  If that's not the desired
> distance, then don't set it as such.  Have you tried the combination I
> suggested in the last message?  Does it give an initial distance of
> 0.815 nm?
>
>> Also as regards to your second point; what if in the initial
>> configurations the two reference groups do not lie along the stated
>> vector?
>>
>
> Hard to say, but probably you'll get some very high forces at the
> outset of the simulation as the simulation as the umbrella potential
> tries to force the pulled group to conform to the restraint
> specifications.  Whether or not that negatively impacts the ultimate
> result of the simulation is also an important consideration.  If
> you're pulling along a given vector, you should start with your
> reference coordinates as close to the desired location as possible.
>
> -Justin
>
>> Cheers
>>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 Justin

 I did a short test on a particular window with the specified vector
 with
 pull_init =0.78nm. I then grompp(ed) the final configuration and it
 gave
 me a distance of 0.78 as the initial ditsance, fair enough. However
 when
 I viewed the final line from g_dist the absolute distance or
 modulus was
 0.815 nm, which agreed with the distance I calculated using a
 molecular
 configuration editor. My question is therefore this, when using
 pull_geometry =direction with a specified vector, How should one
 interpret the initial distance provided by grompp? and how does
 Gromacs
 deal with the fact that the vector between the two point changes
 during
 the run ?

>>> You're telling grompp that the initial distance is 0.78 nm, so it's
>>> spitting that back out.  If that's not the true distance, then specify
>>> the correct quantity :)  The distance should be correctly detected
>>> with:
>>>
>>> pull_start = yes
>>> pull_init = 0
>>>
>>> As for the second question, the vector doesn't change over the
>>> simulation, but the position of pull_group1 along that vector will.
>>> That's what the umbrella potential is doing - it allows for harmonic
>>> oscillation along any of the dimensions specified by pull_vec/pull_dim
>>> (depending on the settings).
>>>
>>> -Justin
>>>
>>
>

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Re: [gmx-users] a question about position restraint time for long alkyl chain molecules

[XUEMING TANG]

Hi Justin

Sorry I did not explain clearly. I apply position restraint to the head
group of surfactant molecules and let all others (solvents and tail of
surfactants) run freely. I am concerning about how long I should restraint
the head group of surfactant molecules. If only concerning the solvent
molecules, 10ps is enough for water to relax. But if concern the tail of the
surfactant molecules, how to calculate the time of restraint (100ps,
500ps...). I guess 500ps position restraint will be enough? Is there any
problem if I restraint the head group of surfactant micelle too long?

Thank you and have a nice day :P

Best!
Xueming

On Wed, Jun 8, 2011 at 12:51 PM, Justin A. Lemkul  wrote:

>
>
> XUEMING TANG wrote:
>
>> Hi there
>>
>> I put a SDS Spherical micelle in solution and want to apply position
>> restraint before mdrun. Here I have a question: For macromolecules like
>> micelles, should the position restraint apply to not only the water
>> molecules (and ions) but also to the surfactant molecules in the micelle? If
>> it is also for the surfactant molecules, how to calculate the position
>> restraint time in this case.
>>
>
> Why would you restrain the solvent?  That basically prevents equilibration
> from happening.  Then, if you restrain the solvent and surfactant, you truly
> accomplish nothing.
>
> Likely the best course of action is to restrain the surfactant molecules,
> while allowing everything else to move freely.  Then, remove all restraints
> and equilibrate a while longer.
>
> -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
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] a question about position restraint time for long alkyl chain molecules

[Justin A. Lemkul]

XUEMING TANG wrote:

Hi Justin

Sorry I did not explain clearly. I apply position restraint to the head 
group of surfactant molecules and let all others (solvents and tail of 
surfactants) run freely. I am concerning about how long I should 
restraint the head group of surfactant molecules. If only concerning the 
solvent molecules, 10ps is enough for water to relax. But if concern the 
tail of the surfactant molecules, how to calculate the time of restraint 
(100ps, 500ps...). I guess 500ps position restraint will be enough? Is 
there any problem if I restraint the head group of surfactant micelle 
too long?




I doubt you can restrain anything too long.  If all the relevant thermodynamic 
observables have converged (T, P, energy, etc), then your restrained 
equilibration is probably sufficient.  Once you remove the restraints, you'll 
have to assess some structural properties of the micelle to know if it is 
equilibrated before collecting data.  Maybe density, size, etc.


-Justin


Thank you and have a nice day :P

Best!
Xueming

On Wed, Jun 8, 2011 at 12:51 PM, Justin A. Lemkul > wrote:




XUEMING TANG wrote:

Hi there

I put a SDS Spherical micelle in solution and want to apply
position restraint before mdrun. Here I have a question: For
macromolecules like micelles, should the position restraint
apply to not only the water molecules (and ions) but also to the
surfactant molecules in the micelle? If it is also for the
surfactant molecules, how to calculate the position restraint
time in this case.


Why would you restrain the solvent?  That basically prevents
equilibration from happening.  Then, if you restrain the solvent and
surfactant, you truly accomplish nothing.

Likely the best course of action is to restrain the surfactant
molecules, while allowing everything else to move freely.  Then,
remove all restraints and equilibrate a while longer.

-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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.
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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] Why does the -append option exist?

[Dimitar Pachov]

Hello,

On Wed, Jun 8, 2011 at 4:21 AM, Sander Pronk  wrote:

> Hi Dimitar,
>
> Thanks for the bug report. Would you mind trying the test program I
> attached on the same file system that you get the truncated files on?
>
> compile it with gcc testje.c -o testio
>

Yes, but no problem:


[dpachov@login-0-0 NEWTEST]$ ./testio
TEST PASSED: ftell gives: 46


As for the other questions:

HPC OS version:

[dpachov@login-0-0 NEWTEST]$ uname -a
Linux login-0-0.local 2.6.18-194.17.1.el5xen #1 SMP Mon Sep 20 07:20:39 EDT
2010 x86_64 x86_64 x86_64 GNU/Linux
[dpachov@login-0-0 NEWTEST]$ cat /etc/redhat-release
Red Hat Enterprise Linux Server release 5.2 (Tikanga)


GROMACS 4.5.4 built:

module purge
module load INTEL/intel-12.0
module load OPENMPI/1.4.3_INTEL_12.0
module load FFTW/2.1.5-INTEL_12.0 # not needed

#
# GROMACS settings

export CC=mpicc
export F77=mpif77
export CXX=mpic++
export FC=mpif90
export F90=mpif90

make distclean

echo "XXX building single prec XX"

./configure
--prefix=/home/dpachov/mymodules/GROMACS/EXEC/4.5.4-INTEL_12.0/SINGLE \
--enable-mpi \
 --enable-shared \
--program-prefix="" --program-suffix="" \
--enable-float --disable-fortran \
--with-fft=mkl \
--with-external-blas \
--with-external-lapack \
--with-gsl \
--without-x \
CFLAGS="-O3 -funroll-all-loops" \
FFLAGS="-O3 -funroll-all-loops" \
CPPFLAGS="-I${MPI_INCLUDE} -I${MKL_INCLUDE} " \
LDFLAGS="-L${MPI_LIB} -L${MKL_LIB} -lmkl_intel_lp64 -lmkl_core
-lmkl_intel_thread -liomp5 "

make -j 8 && make install


Just did the same test on Hopper 2:
http://www.nersc.gov/users/computational-systems/hopper/

with their built GROMACS 4.5.3 (gromacs/4.5.3(default)), and the result was
the same as reported earlier. You could do the test there as well, if you
have access, and see what you would get.

Hope that helps a bit.

Thanks,
Dimitar





>
> Sander
>
>
>
>
>
> On Jun 7, 2011, at 23:21 , Dimitar Pachov wrote:
>
> Hello,
>
> Just a quick update after a few shorts tests we (my colleague and I)
> quickly did. First, using
>
> "*You can emulate this yourself by calling "sleep 10s" before mdrun and
> see if that's long enough to solve the latency issue in your case.*"
>
> doesn't work for a few reasons, mainly because it doesn't seem to be a
> latency issue, but also because the load on a node is not affected by
> "sleep".
>
> However, you can reproduce the behavior I have observed pretty easily. It
> seems to be related to the values of the pointers to the *xtc, *trr, *edr,
> etc files written at the end of the checkpoint file after abrupt crashes AND
> to the frequency of access (opening) to those files. How to test:
>
> 1. In your input *mdp file put a high frequency of saving coordinates to,
> say, the *xtc (10, for example) and a low frequency for the *trr file
> (10,000, for example).
> 2. Run GROMACS (mdrun -s run.tpr -v -cpi -deffnm run)
> 3. Kill abruptly the run shortly after that (say, after 10-100 steps).
> 4. You should have a few frames written in the *xtc file, and the only one
> (the first) in the *trr file. The *cpt file should have different from zero
> values for "file_offset_low" for all of these files (the pointers have been
> updated).
>
> 5. Restart GROMACS (mdrun -s run.tpr -v -cpi -deffnm run).
> 6. Kill abruptly the run shortly after that (say, after 10-100 steps). Pay
> attention that the frequency for accessing/writing the *trr has not been
> reached.
> 7. You should have a few additional frames written in the *xtc file, while
> the *trr will still have only 1 frame (the first). The *cpt file now has
> updated all pointer values "file_offset_low", BUT the pointer to the *trr
> has acquired a value of 0. Obviously, we already now what will happen if we
> restart again from this last *cpt file.
>
> 8. Restart GROMACS (mdrun -s run.tpr -v -cpi -deffnm run).
> 9. Kill it.
> 10. File *trr has size zero.
>
>
> Therefore, if a run is killed before the files are accessed for writing
> (depending on the chosen frequency), the file offset values reported in the
> *cpt file doesn't seem to be accordingly updated, and hence a new restart
> inevitably leads to overwritten output files.
>
> Do you think this is fixable?
>
> Thanks,
> Dimitar
>
>
>
>
>
>
> On Sun, Jun 5, 2011 at 6:20 PM, Roland Schulz  wrote:
>
>> Two comments about the discussion:
>>
>> 1) I agree that buffered output (Kernel buffers - not application buffers)
>> should not affect I/O. If it does it should be filed as bug to the OS. Maybe
>> someone can write a short test application which tries to reproduce this
>> idea. Thus writing to a file from one node and immediate after one test
>> program is killed on one node writing to it from some other node.
>>
>> 2) We lock files but only the log file. The idea is that we only need
>> to guarantee that the set of files is only accessed by one application. This
>> seems safe but in case someone sees a way of how the trajectory is opened
>> without the log file being opened, please file a bu

Re: [gmx-users] Re: distance/direction PMF

[Justin A. Lemkul]

Gavin Melaugh wrote:

Yeah

 I set pull_init =0, and pull_start = yes, and it still gave a "distance
at start" as 0.78nm. It must be doing something funny because with
pull_vec, because when I use pull_geometry = distance and pull_dim
= Y Y Y, the distance 0.815nm is returned as the "distance at start",
which is the actual distance between the two groups.



I have no idea why this is happening.  If you'd like me to troubleshoot further 
and see if I can get to the bottom of this, please send me (off-list is OK):


1. Coordinate file
2. Topology file(s)
3. The .mdp file that is giving the weird result

-Justin


Cheers

Gavin
 
Justin A. Lemkul wrote:


Gavin Melaugh wrote:

Hi Justin

Sorry maybe I was unclear before with my first point; the specified
distance in the mdp file is 0.78nm, which grompp returns back as the ref
distance. The "distance at the start" that grompp returns is also
0.78nm, even though the actual distance is 0.815nm. That's why I was
asking what this distance actually means, as it is not the absolute
distance between the reference groups.

As I said before, you're telling grompp to make that the reference
distance. You say "the specified distance in the mdp file is 0.78 nm,"
therefore grompp is doing what it's told.  If that's not the desired
distance, then don't set it as such.  Have you tried the combination I
suggested in the last message?  Does it give an initial distance of
0.815 nm?


Also as regards to your second point; what if in the initial
configurations the two reference groups do not lie along the stated
vector?


Hard to say, but probably you'll get some very high forces at the
outset of the simulation as the simulation as the umbrella potential
tries to force the pulled group to conform to the restraint
specifications.  Whether or not that negatively impacts the ultimate
result of the simulation is also an important consideration.  If
you're pulling along a given vector, you should start with your
reference coordinates as close to the desired location as possible.

-Justin


Cheers

Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Justin

I did a short test on a particular window with the specified vector
with
pull_init =0.78nm. I then grompp(ed) the final configuration and it
gave
me a distance of 0.78 as the initial ditsance, fair enough. However
when
I viewed the final line from g_dist the absolute distance or
modulus was
0.815 nm, which agreed with the distance I calculated using a
molecular
configuration editor. My question is therefore this, when using
pull_geometry =direction with a specified vector, How should one
interpret the initial distance provided by grompp? and how does
Gromacs
deal with the fact that the vector between the two point changes
during
the run ?


You're telling grompp that the initial distance is 0.78 nm, so it's
spitting that back out.  If that's not the true distance, then specify
the correct quantity :)  The distance should be correctly detected
with:

pull_start = yes
pull_init = 0

As for the second question, the vector doesn't change over the
simulation, but the position of pull_group1 along that vector will.
That's what the umbrella potential is doing - it allows for harmonic
oscillation along any of the dimensions specified by pull_vec/pull_dim
(depending on the settings).

-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] a question about position restraint time for long alkyl chain molecules

[XUEMING TANG]

Got it (cool :)), Thank you!!!
Best!
Xueming

On Wed, Jun 8, 2011 at 1:15 PM, Justin A. Lemkul  wrote:

>
>
> XUEMING TANG wrote:
>
>> Hi Justin
>>
>> Sorry I did not explain clearly. I apply position restraint to the head
>> group of surfactant molecules and let all others (solvents and tail of
>> surfactants) run freely. I am concerning about how long I should restraint
>> the head group of surfactant molecules. If only concerning the solvent
>> molecules, 10ps is enough for water to relax. But if concern the tail of the
>> surfactant molecules, how to calculate the time of restraint (100ps,
>> 500ps...). I guess 500ps position restraint will be enough? Is there any
>> problem if I restraint the head group of surfactant micelle too long?
>>
>>
> I doubt you can restrain anything too long.  If all the relevant
> thermodynamic observables have converged (T, P, energy, etc), then your
> restrained equilibration is probably sufficient.  Once you remove the
> restraints, you'll have to assess some structural properties of the micelle
> to know if it is equilibrated before collecting data.  Maybe density, size,
> etc.
>
> -Justin
>
>  Thank you and have a nice day :P
>>
>> Best!
>> Xueming
>>
>> On Wed, Jun 8, 2011 at 12:51 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>XUEMING TANG wrote:
>>
>>Hi there
>>
>>I put a SDS Spherical micelle in solution and want to apply
>>position restraint before mdrun. Here I have a question: For
>>macromolecules like micelles, should the position restraint
>>apply to not only the water molecules (and ions) but also to the
>>surfactant molecules in the micelle? If it is also for the
>>surfactant molecules, how to calculate the position restraint
>>time in this case.
>>
>>
>>Why would you restrain the solvent?  That basically prevents
>>equilibration from happening.  Then, if you restrain the solvent and
>>surfactant, you truly accomplish nothing.
>>
>>Likely the best course of action is to restrain the surfactant
>>molecules, while allowing everything else to move freely.  Then,
>>remove all restraints and equilibrate a while longer.
>>
>>-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
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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] oplsaa vs. charmm

[Michael Daily]

  
  
Do you have some experimental data to compare to your IDP
simulations, like X-ray scattering or some such? I'd imagine that
IDP simulations with either forcefield would only be qualitatively
accurate given that the forcefields are calibrated, as you say, on
rigid proteins and small molecules.

On 6/8/11 8:00 AM, Thomas Evangelidis wrote:
Dear Prof van der Spoel and GROMACS users,
  
  I have read the article "Scrutinizing Molecular Mechanics Force
  Fields..." where it is demonstrated that AMBER99sb yields protein
  conformations that are in better agreement with residual dipolar
  coupling, J-coupling and NOE data, compared with other force
  fields. However, both proteins used for this benchmark study
  (ubiquitin and protein G) are rather rigid, so I was wondering if
  there is a similar analysis for flexible proteins/peptides. I want
  to simulate a few intrinsically disordered proteins/peptides of
  length between 40 and 100 aa and would like to know what would be
  the best choice of force field to use. Any experience or knowledge
  on this matter would be greatly appreciated!
  
  thanks in advance,
  Thomas
  
  
  
  On 27 May 2011 19:01, David van der Spoel

wrote:

  
On 2011-05-27 17.50, simon sham wrote:
  
Hi,
I have recently done two simulations on a protein at
high temperature
near its melting temperature. At the beginning I used
CHARMM forcefield,
and then OPLSAA to double check the results. There are
some differences
in the structures between the forcefield used. I know
different
forcefields can give different results. All parameters
in the
simulations were the same except the forcefield. Is
there anyway I can
tell which forcefield gives more reliable results?

Thanks for the insights,

Simon

  

  
  You might want to check
  
  Oliver Lange, David van der Spoel and Bert de Groot:
  Scrutinizing Molecular Mechanics Force Fields on the
  Microsecond Timescale With NMR Data Biophys. J. 99 pp. 647-655
  (2010)
  
  where we compare a number of FFs to NMR data.
  

-- 
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.se    http://folding.bmc.uu.se
  

  -- 
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  http://lists.gromacs.org/mailman/listinfo/gmx-users
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  -- 
  ==
  Thomas Evangelidis
  PhD student
  Biomedical Research
Foundation, Academy of Athens
  4 Soranou Ephessiou ,
115 27
Athens, Greece

email: tev...@bioacademy.gr
    teva...@gmail.com
  
website:
https://sites.google.com/site/thomasevangelidishomepage/
  
  
  



-- 
Michael D. Daily, Ph.D.
Postdoctoral Fellow
Qiang Cui group
Department of Chemistry
University of Wisconsin-Madison
  

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Re: [gmx-users] oplsaa vs. charmm

[Da-Wei Li]

I really don't think you can get adequate sampling for IDPs that have 40
residues, using full atomic MD.


On Wed, Jun 8, 2011 at 3:25 PM, Michael Daily  wrote:

>  Do you have some experimental data to compare to your IDP simulations,
> like X-ray scattering or some such? I'd imagine that IDP simulations with
> either forcefield would only be qualitatively accurate given that the
> forcefields are calibrated, as you say, on rigid proteins and small
> molecules.
>
> On 6/8/11 8:00 AM, Thomas Evangelidis wrote:
>
> Dear Prof van der Spoel and GROMACS users,
>
> I have read the article "Scrutinizing Molecular Mechanics Force Fields..."
> where it is demonstrated that AMBER99sb yields protein conformations that
> are in better agreement with residual dipolar coupling, J-coupling and NOE
> data, compared with other force fields. However, both proteins used for this
> benchmark study (ubiquitin and protein G) are rather rigid, so I was
> wondering if there is a similar analysis for flexible proteins/peptides. I
> want to simulate a few intrinsically disordered proteins/peptides of length
> between 40 and 100 aa and would like to know what would be the best choice
> of force field to use. Any experience or knowledge on this matter would be
> greatly appreciated!
>
> thanks in advance,
> Thomas
>
>
>
> On 27 May 2011 19:01, David van der Spoel  wrote:
>
>>  On 2011-05-27 17.50, simon sham wrote:
>>
>>> Hi,
>>> I have recently done two simulations on a protein at high temperature
>>> near its melting temperature. At the beginning I used CHARMM forcefield,
>>> and then OPLSAA to double check the results. There are some differences
>>> in the structures between the forcefield used. I know different
>>> forcefields can give different results. All parameters in the
>>> simulations were the same except the forcefield. Is there anyway I can
>>> tell which forcefield gives more reliable results?
>>>
>>> Thanks for the insights,
>>>
>>> Simon
>>>
>>>   You might want to check
>>
>> Oliver Lange, David van der Spoel and Bert de Groot: Scrutinizing
>> Molecular Mechanics Force Fields on the Microsecond Timescale With NMR Data
>> Biophys. J. 99 pp. 647-655 (2010)
>>
>> where we compare a number of FFs to NMR data.
>>
>> --
>> 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
>>
>
>
>
> --
>
> ==
>
> Thomas Evangelidis
>
> PhD student
>
> Biomedical Research Foundation, Academy of Athens
>
> 4 Soranou Ephessiou , 115 27 Athens, Greece
>
> email: tev...@bioacademy.gr
>
>   teva...@gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
>
>
> --
> Michael D. Daily, Ph.D.
> Postdoctoral Fellow
> Qiang Cui group
> Department of Chemistry
> University of Wisconsin-Madison
>
>
> --
> 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!
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>
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Re: [gmx-users] oplsaa vs. charmm

[Justin A. Lemkul]

Da-Wei Li wrote:
I really don't think you can get adequate sampling for IDPs that have 40 
residues, using full atomic MD.




I disagree.  Perhaps brute force MD would not accomplish the task (unless you 
have considerable resources and don't want your answers very quickly, but even 
then...), but there are certainly a number of techniques, including implicit 
solvent, REMD, generalized Hamiltonian replica exchange, and fancy umbrella 
sampling and/or free energy settings that can vastly improve sampling for such 
systems.


-Justin



On Wed, Jun 8, 2011 at 3:25 PM, Michael Daily > wrote:


Do you have some experimental data to compare to your IDP
simulations, like X-ray scattering or some such? I'd imagine that
IDP simulations with either forcefield would only be qualitatively
accurate given that the forcefields are calibrated, as you say, on
rigid proteins and small molecules.

On 6/8/11 8:00 AM, Thomas Evangelidis wrote:

Dear Prof van der Spoel and GROMACS users,

I have read the article "Scrutinizing Molecular Mechanics Force
Fields..." where it is demonstrated that AMBER99sb yields protein
conformations that are in better agreement with residual dipolar
coupling, J-coupling and NOE data, compared with other force
fields. However, both proteins used for this benchmark study
(ubiquitin and protein G) are rather rigid, so I was wondering if
there is a similar analysis for flexible proteins/peptides. I want
to simulate a few intrinsically disordered proteins/peptides of
length between 40 and 100 aa and would like to know what would be
the best choice of force field to use. Any experience or knowledge
on this matter would be greatly appreciated!

thanks in advance,
Thomas



On 27 May 2011 19:01, David van der Spoel mailto:sp...@xray.bmc.uu.se>> wrote:

On 2011-05-27 17.50, simon sham wrote:

Hi,
I have recently done two simulations on a protein at high
temperature
near its melting temperature. At the beginning I used
CHARMM forcefield,
and then OPLSAA to double check the results. There are
some differences
in the structures between the forcefield used. I know
different
forcefields can give different results. All parameters in the
simulations were the same except the forcefield. Is there
anyway I can
tell which forcefield gives more reliable results?

Thanks for the insights,

Simon

You might want to check

Oliver Lange, David van der Spoel and Bert de Groot:
Scrutinizing Molecular Mechanics Force Fields on the
Microsecond Timescale With NMR Data Biophys. J. 99 pp. 647-655
(2010)

where we compare a number of FFs to NMR data.

-- 
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.se   
 http://folding.bmc.uu.se


-- 
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-- 


==

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tev...@bioacademy.gr 

  teva...@gmail.com 


website: https://sites.google.com/site/thomasevangelidishomepage/






-- 
Michael D. Daily, Ph.D.

Postdoctoral Fellow
Qiang Cui group
Department of Chemistry
University of Wisconsin-Madison


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--


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

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

[Igor Marques]

thomas,

i've recently placed a similar question and justin asked me to show my index
for the double bound calculation, so, i'm asking you the same.
you should have

> Ci-1
> Ci - the first carbon of the double bound
> Ci+1 - the second carbon of the double bound
> Ci+2
>
in that index

doing this, for C9 and C10 i've obtained the following values
 0.0738068
  -0.000533683

that you should then replace in the correct positions in the sn2 output


good luck,
and sorry if i'm missing the point :|


igor


  Igor Marques


On Wed, Jun 8, 2011 at 5:53 PM, Thomas Piggot  wrote:

> Hi Everyone,
>
> I am facing a problem when calculating the lipid deuterium order parameters
> for the unsaturated carbons of the sn-2 tail of POPC using g_order with
> GROMACS version 4.5.4 (although I have tried other older versions too but
> they all give the same results).
>
> Firstly, I should say the the calculation of the order parameters for the
> saturated sn-1 chain (and also both chains of DPPC) behave as I would
> expect, and produce order parameters that compare well to previously
> published simulations and experimental values.
>
> To calculate the order parameters of the unsaturated chain I am following
> the approach as given on the GROMACS website (
> http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order), so
> splitting the calculation into two parts for the saturated and unsaturated
> regions of the chain. The problem I am facing is that the order parameter
> for carbon 9 (so the first carbon in the double bond), calculated using the
> -unsat option, is much larger than expected. By this I mean that for the two
> different force fields I have tested (namely the CHARMM36 parameters of
> Klauda et al., and the GROMOS 53A6L parameters of Poger et al.) the order
> parameter for this carbon is much larger than the published simulation
> values and also much larger than experimental values. To highlight this, I
> have just put the numbers I have obtained using g_order for this carbon
> below, and compared to some rough values I have estimated from figures
> provided in the Klauda and Poger papers:
>
> CHARMM36
>
> g_order:0.133732
> Klauda estimate:0.06
>
>
> GROMOS53A6L:
>
> g_order:0.199651
> Poger estimate: 0.07
>
> Myself and a colleague have tried looking into the code to determine how
> the order parameters are calculated using the -unsat option, however we
> couldn't quite follow the calculation. Hopefully someone who knows something
> more about g_order can help with this problem. Again I should stress that it
> appears that the main difference in order parameters between what I have
> calculated and the published ones is just in this one carbon, for both force
> fields. A similar issue to this has also been reported previously on the
> list for this carbon of POPC using the 'Berger' force field (
> http://lists.gromacs.org/pipermail/gmx-users/2010-February/049072.html).
>
> Thank you for any help anyone can give
>
> Cheers
>
> Tom
>
> --
> Dr Thomas Piggot
> University of Southampton, UK.
> --
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Umbrella sampling of phosphate ion binding

[bharat gupta]

Hi Justin,

I am having following doubts regarding umbrella sampling of phosphate ion
binding to my protein .

1. As per the tutorial, I need to fix an immobile reference. In my case
which region do I have to fix as my protein consists of one single chain.
Since  I am studying the binding and unbinding of ion, shall I fix the ion
fixed. If it's so, then do I have to give a different chain name for it as
my complex doesnot chain name for ion/ligand.

2. What should be the size of box and how do I know where to place the
protein's COM in box (the precise location).



Pls reply so that I can move further with the procedure



-- 
Bharat
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Re: [gmx-users] Umbrella sampling of phosphate ion binding

[Justin A. Lemkul]

bharat gupta wrote:

Hi Justin,

I am having following doubts regarding umbrella sampling of phosphate 
ion binding to my protein .


1. As per the tutorial, I need to fix an immobile reference. In my case 
which region do I have to fix as my protein consists of one single 
chain. Since  I am studying the binding and unbinding of ion, shall I 
fix the ion fixed. If it's so, then do I have to give a different chain 
name for it as my complex doesnot chain name for ion/ligand.




You don't need an immobile reference just because my tutorial did.  I had a 
particular need to do so.  For your purpose, I highly doubt it's necessary. 
You're looking at small molecule-protein interactions, not protein-protein 
interactions.


2. What should be the size of box and how do I know where to place the 
protein's COM in box (the precise location).




The absolute COM is somewhat irrelevant; all distances during pulling are 
relative.  You can place the protein in a certain location in the box for 
convenience if you like.  The box size must be greater than twice the pull 
distance, as explained in the tutorial.  The amount that you wish to pull will 
dictate both the location of the protein and the box size.


-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] Umbrella sampling of phosphate ion binding

[bharat gupta]

does the gromacs force field has topology and ff parameter for H2PO4(-) ion
. As I have derived both topology and FF parameter from prodrug server and
after checking the topology I found that it has deleted of the hydrogen.

On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul  wrote:

>
>
> bharat gupta wrote:
>
>> Hi Justin,
>>
>> I am having following doubts regarding umbrella sampling of phosphate ion
>> binding to my protein .
>>
>> 1. As per the tutorial, I need to fix an immobile reference. In my case
>> which region do I have to fix as my protein consists of one single chain.
>> Since  I am studying the binding and unbinding of ion, shall I fix the ion
>> fixed. If it's so, then do I have to give a different chain name for it as
>> my complex doesnot chain name for ion/ligand.
>>
>>
> You don't need an immobile reference just because my tutorial did.  I had a
> particular need to do so.  For your purpose, I highly doubt it's necessary.
> You're looking at small molecule-protein interactions, not protein-protein
> interactions.
>
>
>  2. What should be the size of box and how do I know where to place the
>> protein's COM in box (the precise location).
>>
>>
> The absolute COM is somewhat irrelevant; all distances during pulling are
> relative.  You can place the protein in a certain location in the box for
> convenience if you like.  The box size must be greater than twice the pull
> distance, as explained in the tutorial.  The amount that you wish to pull
> will dictate both the location of the protein and the box size.
>
> -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/Searchbefore
>  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 
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>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] Umbrella sampling of phosphate ion binding

[Justin A. Lemkul]

bharat gupta wrote:
does the gromacs force field has topology and ff parameter for H2PO4(-) 
ion . As I have derived both topology and FF parameter from prodrug 


Probably not; check the .rtp file for your desired force field.

server and after checking the topology I found that it has deleted of 
the hydrogen.




See the PRODRG FAQ; this gets asked all the time.

http://davapc1.bioch.dundee.ac.uk/prodrg/prodrg_faq.html

No matter what PRODRG gives you, the charges will probably be useless anyway:

http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

So you're in for the difficult process of parameterization if no one's already 
developed parameters for your molecule:


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

-Justin

On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul > wrote:




bharat gupta wrote:

Hi Justin,

I am having following doubts regarding umbrella sampling of
phosphate ion binding to my protein .

1. As per the tutorial, I need to fix an immobile reference. In
my case which region do I have to fix as my protein consists of
one single chain. Since  I am studying the binding and unbinding
of ion, shall I fix the ion fixed. If it's so, then do I have to
give a different chain name for it as my complex doesnot chain
name for ion/ligand.


You don't need an immobile reference just because my tutorial did.
 I had a particular need to do so.  For your purpose, I highly doubt
it's necessary. You're looking at small molecule-protein
interactions, not protein-protein interactions.


2. What should be the size of box and how do I know where to
place the protein's COM in box (the precise location).


The absolute COM is somewhat irrelevant; all distances during
pulling are relative.  You can place the protein in a certain
location in the box for convenience if you like.  The box size must
be greater than twice the pull distance, as explained in the
tutorial.  The amount that you wish to pull will dictate both the
location of the protein and the box size.

-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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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


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] Umbrella sampling of phosphate ion binding

[bharat gupta]

I found it in the /shared/top/ gmx.ff folder . Here's the file

;
; Force field based on GROMOS with new charges as described in
; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen:
; Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic
; mottle virus coat protein in solution with phosphate ions
; Biophys. J. 71 pp. 2920-2932 (1996)
;
[ moleculetype ]
; name  nrexcl
h2po44

[ atoms ]
;   nrtype   resnr  residuatomcgnrcharge  mass
; use charges from Janez Mavri
 1  OA   1 PI   O1   1-0.777
 2  OA   1 PI   O2   1-0.777
 3  OM   1 PI   O3   1-0.943
 4  OM   1 PI   O4   1-0.943
 5   P   1 PIP   1 1.596
 6  HO   1 PI   H1   1 0.422
 7  HO   1 PI   H2   1 0.422

[ bonds ]
;  aiaj funct   c0   c1
5 1 1 1.637000e-01
5 2 1 1.637000e-01
5 3 1 1.478000e-01
5 4 1 1.478000e-01
6 1 1 0.943000e-01
7 2 1 0.943000e-01

[ angles ]
;  aiajak funct   c0 c1
2 5 1 1 1.015000e+02 400
3 5 1 1 1.059000e+02
4 5 1 1 1.082000e+02
3 5 2 1 1.059000e+02
4 5 2 1 1.082000e+02
4 5 3 1 1.248000e+02
6 1 5 1 1.082000e+02
7 2 5 1 1.082000e+02

[ dihedrals ]
;  aiajakal funct
6 1 5 2 1
7 2 5 1 1

Can I use it or not ??

On Thu, Jun 9, 2011 at 10:26 AM, Justin A. Lemkul  wrote:

>
>
> bharat gupta wrote:
>
>> does the gromacs force field has topology and ff parameter for H2PO4(-)
>> ion . As I have derived both topology and FF parameter from prodrug
>>
>
> Probably not; check the .rtp file for your desired force field.
>
>
>  server and after checking the topology I found that it has deleted of the
>> hydrogen.
>>
>>
> See the PRODRG FAQ; this gets asked all the time.
>
> http://davapc1.bioch.dundee.**ac.uk/prodrg/prodrg_faq.html
>
> No matter what PRODRG gives you, the charges will probably be useless
> anyway:
>
> http://www.gromacs.org/**Downloads/Related_Software/**PRODRG#Tips
>
> So you're in for the difficult process of parameterization if no one's
> already developed parameters for your molecule:
>
> http://www.gromacs.org/**Documentation/How-tos/**Parameterization
>
> -Justin
>
>  On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>bharat gupta wrote:
>>
>>Hi Justin,
>>
>>I am having following doubts regarding umbrella sampling of
>>phosphate ion binding to my protein .
>>
>>1. As per the tutorial, I need to fix an immobile reference. In
>>my case which region do I have to fix as my protein consists of
>>one single chain. Since  I am studying the binding and unbinding
>>of ion, shall I fix the ion fixed. If it's so, then do I have to
>>give a different chain name for it as my complex doesnot chain
>>name for ion/ligand.
>>
>>
>>You don't need an immobile reference just because my tutorial did.
>> I had a particular need to do so.  For your purpose, I highly doubt
>>it's necessary. You're looking at small molecule-protein
>>interactions, not protein-protein interactions.
>>
>>
>>2. What should be the size of box and how do I know where to
>>place the protein's COM in box (the precise location).
>>
>>
>>The absolute COM is somewhat irrelevant; all distances during
>>pulling are relative.  You can place the protein in a certain
>>location in the box for convenience if you like.  The box size must
>>be greater than twice the pull distance, as explained in the
>>tutorial.  The amount that you wish to pull will dictate both the
>>location of the protein and the box size.
>>
>>-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

Re: [gmx-users] Umbrella sampling of phosphate ion binding

[Justin A. Lemkul]

bharat gupta wrote:

I found it in the /shared/top/ gmx.ff folder . Here's the file

;
; Force field based on GROMOS with new charges as described in
; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen:
; Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic
; mottle virus coat protein in solution with phosphate ions
; Biophys. J. 71 pp. 2920-2932 (1996)
;
[ moleculetype ]
; name  nrexcl
h2po44

[ atoms ]
;   nrtype   resnr  residuatomcgnrcharge  mass
; use charges from Janez Mavri
 1  OA   1 PI   O1   1-0.777
 2  OA   1 PI   O2   1-0.777
 3  OM   1 PI   O3   1-0.943
 4  OM   1 PI   O4   1-0.943
 5   P   1 PIP   1 1.596
 6  HO   1 PI   H1   1 0.422
 7  HO   1 PI   H2   1 0.422

[ bonds ]
;  aiaj funct   c0   c1
5 1 1 1.637000e-01
5 2 1 1.637000e-01
5 3 1 1.478000e-01
5 4 1 1.478000e-01
6 1 1 0.943000e-01
7 2 1 0.943000e-01

[ angles ]
;  aiajak funct   c0 c1
2 5 1 1 1.015000e+02 400
3 5 1 1 1.059000e+02
4 5 1 1 1.082000e+02
3 5 2 1 1.059000e+02
4 5 2 1 1.082000e+02
4 5 3 1 1.248000e+02
6 1 5 1 1.082000e+02
7 2 5 1 1.082000e+02

[ dihedrals ]
;  aiajakal funct
6 1 5 2 1
7 2 5 1 1

Can I use it or not ??



Not likely.  Please read in the manual about why the gmx.ff force field should 
not be used.


-Justin

On Thu, Jun 9, 2011 at 10:26 AM, Justin A. Lemkul > wrote:




bharat gupta wrote:

does the gromacs force field has topology and ff parameter for
H2PO4(-) ion . As I have derived both topology and FF parameter
from prodrug


Probably not; check the .rtp file for your desired force field.


server and after checking the topology I found that it has
deleted of the hydrogen.


See the PRODRG FAQ; this gets asked all the time.

http://davapc1.bioch.dundee.__ac.uk/prodrg/prodrg_faq.html


No matter what PRODRG gives you, the charges will probably be
useless anyway:

http://www.gromacs.org/__Downloads/Related_Software/__PRODRG#Tips


So you're in for the difficult process of parameterization if no
one's already developed parameters for your molecule:

http://www.gromacs.org/__Documentation/How-tos/__Parameterization


-Justin

On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   bharat gupta wrote:

   Hi Justin,

   I am having following doubts regarding umbrella sampling of
   phosphate ion binding to my protein .

   1. As per the tutorial, I need to fix an immobile
reference. In
   my case which region do I have to fix as my protein
consists of
   one single chain. Since  I am studying the binding and
unbinding
   of ion, shall I fix the ion fixed. If it's so, then do I
have to
   give a different chain name for it as my complex doesnot
chain
   name for ion/ligand.


   You don't need an immobile reference just because my tutorial
did.
I had a particular need to do so.  For your purpose, I
highly doubt
   it's necessary. You're looking at small molecule-protein
   interactions, not protein-protein interactions.


   2. What should be the size of box and how do I know where to
   place the protein's COM in box (the precise location).


   The absolute COM is somewhat irrelevant; all distances during
   pulling are relative.  You can place the protein in a certain
   location in the box for convenience if you like.  The box
size must
   be greater than twice the pull distance, as explained in the
   tutorial.  The amount that you wish to pull will dictate both the
   location of the protein and the box size.

   -Justin

   -- ====

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu 

Re: [gmx-users] Umbrella sampling of phosphate ion binding

[bharat gupta]

Yes, I read the prodrug faqs... then in that case I have to parametrize the
ion ... According to you there is no other way of doing it ??

On Thu, Jun 9, 2011 at 10:30 AM, Justin A. Lemkul  wrote:

>
>
> bharat gupta wrote:
>
>> I found it in the /shared/top/ gmx.ff folder . Here's the file
>>
>> ;
>> ; Force field based on GROMOS with new charges as described in
>> ; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen:
>> ; Molecular modeling of the RNA binding N-terminal part of cowpea
>> chlorotic
>> ; mottle virus coat protein in solution with phosphate ions
>> ; Biophys. J. 71 pp. 2920-2932 (1996)
>> ;
>> [ moleculetype ]
>> ; name  nrexcl
>> h2po44
>>
>> [ atoms ]
>> ;   nrtype   resnr  residuatomcgnrcharge  mass
>> ; use charges from Janez Mavri
>> 1  OA   1 PI   O1   1-0.777
>> 2  OA   1 PI   O2   1-0.777
>> 3  OM   1 PI   O3   1-0.943
>> 4  OM   1 PI   O4   1-0.943
>> 5   P   1 PIP   1 1.596
>> 6  HO   1 PI   H1   1 0.422
>> 7  HO   1 PI   H2   1 0.422
>>
>> [ bonds ]
>> ;  aiaj funct   c0   c1
>>5 1 1 1.637000e-01
>>5 2 1 1.637000e-01
>>5 3 1 1.478000e-01
>>5 4 1 1.478000e-01
>>6 1 1 0.943000e-01
>>7 2 1 0.943000e-01
>>
>> [ angles ]
>> ;  aiajak funct   c0 c1
>>2 5 1 1 1.015000e+02 400
>>3 5 1 1 1.059000e+02
>>4 5 1 1 1.082000e+02
>>3 5 2 1 1.059000e+02
>>4 5 2 1 1.082000e+02
>>4 5 3 1 1.248000e+02
>>6 1 5 1 1.082000e+02
>>7 2 5 1 1.082000e+02
>>
>> [ dihedrals ]
>> ;  aiajakal funct
>>6 1 5 2 1
>>7 2 5 1 1
>>
>> Can I use it or not ??
>>
>>
> Not likely.  Please read in the manual about why the gmx.ff force field
> should not be used.
>
> -Justin
>
>  On Thu, Jun 9, 2011 at 10:26 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>bharat gupta wrote:
>>
>>does the gromacs force field has topology and ff parameter for
>>H2PO4(-) ion . As I have derived both topology and FF parameter
>>from prodrug
>>
>>
>>Probably not; check the .rtp file for your desired force field.
>>
>>
>>server and after checking the topology I found that it has
>>deleted of the hydrogen.
>>
>>
>>See the PRODRG FAQ; this gets asked all the time.
>>
>>
>> http://davapc1.bioch.dundee.__**ac.uk/prodrg/prodrg_faq.html
>>
>> 
>> >
>>
>>No matter what PRODRG gives you, the charges will probably be
>>useless anyway:
>>
>>
>> http://www.gromacs.org/__**Downloads/Related_Software/__**PRODRG#Tips
>>
>> 
>> >
>>
>>So you're in for the difficult process of parameterization if no
>>one's already developed parameters for your molecule:
>>
>>
>> http://www.gromacs.org/__**Documentation/How-tos/__**Parameterization
>>
>> 
>> >
>>
>>-Justin
>>
>>On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   bharat gupta wrote:
>>
>>   Hi Justin,
>>
>>   I am having following doubts regarding umbrella sampling of
>>   phosphate ion binding to my protein .
>>
>>   1. As per the tutorial, I need to fix an immobile
>>reference. In
>>   my case which region do I have to fix as my protein
>>consists of
>>   one single chain. Since  I am studying the binding and
>>unbinding
>>   of ion, shall I fix the ion fixed. If it's so, then do I
>>have to
>>   give a different chain name for it as my complex doesnot
>>chain
>>   name for ion/ligand.
>>
>>
>>   You don't need an immobile reference just because my tutorial
>>did.
>>I had a particular need to do so.  For your purpose, I
>>highly doubt
>>   it's necessary. You're looking at small molecule-protein
>>   interactions, not protein-protein interactions.
>>
>>
>>   2. What should

Re: [gmx-users] Umbrella sampling of phosphate ion binding

[Justin A. Lemkul]

bharat gupta wrote:
Yes, I read the prodrug faqs... then in that case I have to parametrize 


So then you should know that the ADDHYD keyword solves your problem, right?


the ion ... According to you there is no other way of doing it ??



I didn't say there was no way to do it.  It just won't be easy (assuming no one 
else has already developed them for your chosen force field - so spend some time 
in the literature).  Read the primary reference for the force field you wish to 
use and derive suitable parameters accordingly.  Plan on spending a fair bit of 
time doing this.  Good parameters don't come easily.


-Justin

On Thu, Jun 9, 2011 at 10:30 AM, Justin A. Lemkul > wrote:




bharat gupta wrote:

I found it in the /shared/top/ gmx.ff folder . Here's the file

;
; Force field based on GROMOS with new charges as described in
; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C.
Berendsen:
; Molecular modeling of the RNA binding N-terminal part of
cowpea chlorotic
; mottle virus coat protein in solution with phosphate ions
; Biophys. J. 71 pp. 2920-2932 (1996)
;
[ moleculetype ]
; name  nrexcl
h2po44

[ atoms ]
;   nrtype   resnr  residuatomcgnrcharge
 mass

; use charges from Janez Mavri
1  OA   1 PI   O1   1-0.777
2  OA   1 PI   O2   1-0.777
3  OM   1 PI   O3   1-0.943
4  OM   1 PI   O4   1-0.943
5   P   1 PIP   1 1.596
6  HO   1 PI   H1   1 0.422
7  HO   1 PI   H2   1 0.422

[ bonds ]
;  aiaj funct   c0   c1
   5 1 1 1.637000e-01
   5 2 1 1.637000e-01
   5 3 1 1.478000e-01
   5 4 1 1.478000e-01
   6 1 1 0.943000e-01
   7 2 1 0.943000e-01

[ angles ]
;  aiajak funct   c0 c1
   2 5 1 1 1.015000e+02 400
   3 5 1 1 1.059000e+02
   4 5 1 1 1.082000e+02
   3 5 2 1 1.059000e+02
   4 5 2 1 1.082000e+02
   4 5 3 1 1.248000e+02
   6 1 5 1 1.082000e+02
   7 2 5 1 1.082000e+02

[ dihedrals ]
;  aiajakal funct
   6 1 5 2 1
   7 2 5 1 1

Can I use it or not ??


Not likely.  Please read in the manual about why the gmx.ff force
field should not be used.

-Justin

On Thu, Jun 9, 2011 at 10:26 AM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   bharat gupta wrote:

   does the gromacs force field has topology and ff
parameter for
   H2PO4(-) ion . As I have derived both topology and FF
parameter
   from prodrug


   Probably not; check the .rtp file for your desired force field.


   server and after checking the topology I found that it has
   deleted of the hydrogen.


   See the PRODRG FAQ; this gets asked all the time.

   http://davapc1.bioch.dundee.ac.uk/prodrg/prodrg_faq.html

   >

   No matter what PRODRG gives you, the charges will probably be
   useless anyway:

 
 http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips


 
 >

   So you're in for the difficult process of parameterization if no
   one's already developed parameters for your molecule:

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


 
 >

   -Justin

   On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

Re: [gmx-users] Gromacs-4.5.4 install error

[Mark Abraham]

On 8/06/2011 7:06 PM, xuji wrote:
> Hi all gmx-users:

Please do not cross-post such questions to gmx-developers. This question
has nothing to do with development.
> I install gromacs-4.5.4, with
> tar xzf gromacs-4.5.4.tar.gz
> cd gromacs-4.5.4
> export MPICC=/usr/mpi/gcc/mvapich2-1.4.1/bin/mpicc
> ./configure --prefix=/home/xuji/bin/gmx_4.5.4/parallel_float
> --enable-mpi --program-suffix=_mpi --without-x --with-fft=fftw3
> --enable-all-static --without-xml --with-pic
> CPPFLAGS=-I/home/xuji/bin/fftw3_f/include/
> LDFLAGS=-L/home/xuji/bin/fftw3_f/lib/
> make -j 8

--enable-all-static and --with-pic might be inconsistent with each other
or with your MVAPICH installation, and might be the reason for your
linker errors. Some older MPICH and MVAPICH versions are known to be
unsuitable for use with GROMACS, even if linking succeeds.

Mark
> but always got following errors:
> Making all in kernel
> make[3]: Entering directory `/home/xuji/src/gromacs-4.5.4/src/kernel'
> /bin/sh ../../libtool --tag=CC --mode=link
> /usr/mpi/gcc/mvapich2-1.4.1/bin/mpicc -O3 -fomit-frame-pointer
> -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops
> -std=gnu99 -L/home/xuji/bin/fftw3_f/lib/ -all-static -o grompp
> grompp.o libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la
> ../gmxlib/libgmx_mpi.la -lnsl -lm
> /usr/mpi/gcc/mvapich2-1.4.1/bin/mpicc -O3 -fomit-frame-pointer
> -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops
> -std=gnu99 -static -o grompp grompp.o -L/home/xuji/bin/fftw3_f/lib/
> ./.libs/libgmxpreprocess_mpi.a
> /home/xuji/src/gromacs-4.5.4/src/mdlib/.libs/libmd_mpi.a
> ../mdlib/.libs/libmd_mpi.a /home/xuji/bin/fftw3_f/lib/libfftw3f.a
> /home/xuji/src/gromacs-4.5.4/src/gmxlib/.libs/libgmx_mpi.a
> ../gmxlib/.libs/libgmx_mpi.a -lnsl -lm
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(simple_pmi.o): In function
> `PMI_Init':
> (.text+0x1690): warning: Using 'gethostbyname' in statically linked
> applications requires at runtime the shared libraries from the glibc
> version used for linking
> /usr/lib64/libc.a(malloc.o): In function `__malloc_check_init':
> (.text+0x13d0): multiple definition of `__malloc_check_init'
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x8c0):
> first defined here
> /usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed
> from 113 in
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o) to 107 in
> /usr/lib64/libc.a(malloc.o)
> /usr/lib64/libc.a(malloc.o): In function `free':
> (.text+0x6da0): multiple definition of `free'
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x3260):
> first defined here
> /usr/bin/ld: Warning: size of symbol `free' changed from 247 in
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o) to 375 in
> /usr/lib64/libc.a(malloc.o)
> /usr/lib64/libc.a(malloc.o): In function `malloc':
> (.text+0x55b0): multiple definition of `malloc'
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x3370):
> first defined here
> /usr/bin/ld: Warning: size of symbol `malloc' changed from 364 in
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o) to 547 in
> /usr/lib64/libc.a(malloc.o)
> /usr/lib64/libc.a(malloc.o): In function `realloc':
> (.text+0x6f20): multiple definition of `realloc'
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x3740):
> first defined here
> /usr/bin/ld: Warning: size of symbol `realloc' changed from 508 in
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o) to 1123
> in /usr/lib64/libc.a(malloc.o)
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mem_hooks.o): In function
> `set_real_munmap_ptr':
> (.text+0x1e): undefined reference to `dlsym'
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mem_hooks.o): In function
> `set_real_munmap_ptr':
> (.text+0x26): undefined reference to `dlerror'
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mem_hooks.o): In function
> `mvapich2_minit':
> (.text+0x14c): undefined reference to `dlerror'
> /usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function
> `load_driver':
> (.text+0xc7): undefined reference to `dlopen'
> /usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function
> `load_driver':
> (.text+0x102): undefined reference to `dlerror'
> /usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function
> `ibverbs_init':
> (.text+0x11af): undefined reference to `dlopen'
> /usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function
> `ibverbs_init':
> (.text+0x11c0): undefined reference to `dlclose'
> /usr/lib64/libibverbs.a(src_libibverbs_la-verbs.o): In function
> `ibv_create_comp_channel':
> (.text+0xb76): undefined reference to `pthread_mutex_trylock'
> collect2: ld returned 1 exit status
> make[3]: *** [grompp] Error 1
> make[3]: Leaving directory `/home/xuji/src/gromacs-4.5.4/src/kernel'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/home/xuji/src/gromacs-4.5.4/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/home/xuji/src/gro

Re: [gmx-users] Umbrella sampling of phosphate ion binding

[Justin A. Lemkul]

bharat gupta wrote:
Sorry to ask this ... If I try SMD with prodrug generated topology for 
the time being , will it be useful to do that ?? As I don't have much 
time as of now to parametrize and do SMD...




That's a great way to waste time.  If you run a simulation with sub-par 
parameters, you'll get questionable results.  Any good reviewer would dismiss 
work done with a lousy underlying model.


-Justin

On Thu, Jun 9, 2011 at 10:42 AM, Justin A. Lemkul > wrote:




bharat gupta wrote:

Yes, I read the prodrug faqs... then in that case I have to
parametrize


So then you should know that the ADDHYD keyword solves your problem,
right?


the ion ... According to you there is no other way of doing it ??


I didn't say there was no way to do it.  It just won't be easy
(assuming no one else has already developed them for your chosen
force field - so spend some time in the literature).  Read the
primary reference for the force field you wish to use and derive
suitable parameters accordingly.  Plan on spending a fair bit of
time doing this.  Good parameters don't come easily.

-Justin

On Thu, Jun 9, 2011 at 10:30 AM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   bharat gupta wrote:

   I found it in the /shared/top/ gmx.ff folder . Here's the
file

   ;
   ; Force field based on GROMOS with new charges as
described in
   ; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C.
   Berendsen:
   ; Molecular modeling of the RNA binding N-terminal part of
   cowpea chlorotic
   ; mottle virus coat protein in solution with phosphate ions
   ; Biophys. J. 71 pp. 2920-2932 (1996)
   ;
   [ moleculetype ]
   ; name  nrexcl
   h2po44

   [ atoms ]
   ;   nrtype   resnr  residuatomcgnr  
 charge mass

   ; use charges from Janez Mavri
   1  OA   1 PI   O1   1-0.777
   2  OA   1 PI   O2   1-0.777
   3  OM   1 PI   O3   1-0.943
   4  OM   1 PI   O4   1-0.943
   5   P   1 PIP   1 1.596
   6  HO   1 PI   H1   1 0.422
   7  HO   1 PI   H2   1 0.422

   [ bonds ]
   ;  aiaj funct   c0   c1
  5 1 1 1.637000e-01
  5 2 1 1.637000e-01
  5 3 1 1.478000e-01
  5 4 1 1.478000e-01
  6 1 1 0.943000e-01
  7 2 1 0.943000e-01

   [ angles ]
   ;  aiajak funct   c0 c1
  2 5 1 1 1.015000e+02 400
  3 5 1 1 1.059000e+02
  4 5 1 1 1.082000e+02
  3 5 2 1 1.059000e+02
  4 5 2 1 1.082000e+02
  4 5 3 1 1.248000e+02
  6 1 5 1 1.082000e+02
  7 2 5 1 1.082000e+02

   [ dihedrals ]
   ;  aiajakal funct
  6 1 5 2 1
  7 2 5 1 1

   Can I use it or not ??


   Not likely.  Please read in the manual about why the gmx.ff force
   field should not be used.

   -Justin

   On Thu, Jun 9, 2011 at 10:26 AM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

   

RE: [gmx-users] Umbrella sampling of phosphate ion binding

[Dallas Warren]

You have been provided there with the reference in which the parameters for the 
molecule were derived.

Read it!

And determine yourself if it is applicable or not to what you are doing and the 
forcefield you are using.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of bharat gupta
Sent: Thursday, 9 June 2011 11:29 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Umbrella sampling of phosphate ion binding

I found it in the /shared/top/ gmx.ff folder . Here's the file

;
; Force field based on GROMOS with new charges as described in
; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen:
; Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic
; mottle virus coat protein in solution with phosphate ions
; Biophys. J. 71 pp. 2920-2932 (1996)
;
[ moleculetype ]
; name  nrexcl
h2po44

[ atoms ]
;   nrtype   resnr  residuatomcgnrcharge  mass
; use charges from Janez Mavri
 1  OA   1 PI   O1   1-0.777
 2  OA   1 PI   O2   1-0.777
 3  OM   1 PI   O3   1-0.943
 4  OM   1 PI   O4   1-0.943
 5   P   1 PIP   1 1.596
 6  HO   1 PI   H1   1 0.422
 7  HO   1 PI   H2   1 0.422

[ bonds ]
;  aiaj funct   c0   c1
5 1 1 1.637000e-01
5 2 1 1.637000e-01
5 3 1 1.478000e-01
5 4 1 1.478000e-01
6 1 1 0.943000e-01
7 2 1 0.943000e-01

[ angles ]
;  aiajak funct   c0 c1
2 5 1 1 1.015000e+02 400
3 5 1 1 1.059000e+02
4 5 1 1 1.082000e+02
3 5 2 1 1.059000e+02
4 5 2 1 1.082000e+02
4 5 3 1 1.248000e+02
6 1 5 1 1.082000e+02
7 2 5 1 1.082000e+02

[ dihedrals ]
;  aiajakal funct
6 1 5 2 1
7 2 5 1 1

Can I use it or not ??
On Thu, Jun 9, 2011 at 10:26 AM, Justin A. Lemkul 
mailto:jalem...@vt.edu>> wrote:


bharat gupta wrote:
does the gromacs force field has topology and ff parameter for H2PO4(-) ion . 
As I have derived both topology and FF parameter from prodrug

Probably not; check the .rtp file for your desired force field.

server and after checking the topology I found that it has deleted of the 
hydrogen.

See the PRODRG FAQ; this gets asked all the time.

http://davapc1.bioch.dundee.ac.uk/prodrg/prodrg_faq.html

No matter what PRODRG gives you, the charges will probably be useless anyway:

http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

So you're in for the difficult process of parameterization if no one's already 
developed parameters for your molecule:

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

-Justin
On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul 
mailto:jalem...@vt.edu> 
>> wrote:



   bharat gupta wrote:

   Hi Justin,

   I am having following doubts regarding umbrella sampling of
   phosphate ion binding to my protein .

   1. As per the tutorial, I need to fix an immobile reference. In
   my case which region do I have to fix as my protein consists of
   one single chain. Since  I am studying the binding and unbinding
   of ion, shall I fix the ion fixed. If it's so, then do I have to
   give a different chain name for it as my complex doesnot chain
   name for ion/ligand.


   You don't need an immobile reference just because my tutorial did.
I had a particular need to do so.  For your purpose, I highly doubt
   it's necessary. You're looking at small molecule-protein
   interactions, not protein-protein interactions.


   2. What should be the size of box and how do I know where to
   place the protein's COM in box (the precise location).


   The absolute COM is somewhat irrelevant; all distances during
   pulling are relative.  You can place the protein in a certain
   location in the box for convenience if you like.  The box size must
   be greater than twice the pull distance, as explained in the
   tutorial.  The amount that you wish to pull will dictate both the
   location of the protein and the box size.

   -Justin

   -- ==__==

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksbu

Re: [gmx-users] Umbrella sampling of phosphate ion binding

[bharat gupta]

Hi,

After searching I have found parameters for phosphorylated tyrosine. And my
experiment also involves that as in this case phosphate ion only binds to
the active site. So, can I use the parameter for umbrella sampling taken
from amber parameter database.

!!index array str
 "Y1P"
!entry.Y1P.unit.atoms table  str name  str type  int typex  int resx
int flags  int seq  int elmnt  dbl chg
 "N" "N" 0 1 131073 1 7 -0.516300
 "H" "H" 0 1 131073 2 1 0.293600
 "CA" "CT" 0 1 131073 3 6 0.275503
 "HA" "H1" 0 1 131073 4 1 0.008223
 "CB" "CT" 0 1 131073 5 6 -0.354052
 "HB2" "HC" 0 1 131073 6 1 0.110326
 "HB3" "HC" 0 1 131073 7 1 0.110326
 "CG" "CA" 0 1 131073 8 6 0.119728
 "CD1" "CA" 0 1 131073 9 6 -0.198938
 "HD1" "HA" 0 1 131073 10 1 0.137143
 "CE1" "CA" 0 1 131073 11 6 -0.284884
 "HE1" "HA" 0 1 131073 12 1 0.177179
 "CZ" "C" 0 1 131073 13 6 0.452616
 "CE2" "CA" 0 1 131073 14 6 -0.284884
 "HE2" "HA" 0 1 131073 15 1 0.177179
 "CD2" "CA" 0 1 131073 16 6 -0.198938
 "HD2" "HA" 0 1 131073 17 1 0.137143
 "OG" "OS" 0 1 131073 18 8 -0.534452
 "P" "P" 0 1 131073 19 15 1.393213
 "O1P" "OH" 0 1 131073 20 8 -0.752821
 "O2P" "O2" 0 1 131073 21 8 -0.822464
 "O3P" "O2" 0 1 131073 22 8 -0.822464
 "H1P" "HO" 0 1 131073 23 1 0.423316
 "C" "C" 0 1 131073 24 6 0.536600
 "O" "O" 0 1 131073 25 8 -0.581900
!entry.Y1P.unit.atomspertinfo table  str pname  str ptype  int ptypex
int pelmnt  dbl pchg
 "N" "N" 0 -1 0.0
 "H" "H" 0 -1 0.0
 "CA" "CT" 0 -1 0.0
 "HA" "H1" 0 -1 0.0
 "CB" "CT" 0 -1 0.0
 "HB2" "HC" 0 -1 0.0
 "HB3" "HC" 0 -1 0.0
 "CG" "CA" 0 -1 0.0
 "CD1" "CA" 0 -1 0.0
 "HD1" "HA" 0 -1 0.0
 "CE1" "CA" 0 -1 0.0
 "HE1" "HA" 0 -1 0.0
 "CZ" "C" 0 -1 0.0
 "CE2" "CA" 0 -1 0.0
 "HE2" "HA" 0 -1 0.0
 "CD2" "CA" 0 -1 0.0
 "HD2" "HA" 0 -1 0.0
 "OG" "OS" 0 -1 0.0
 "P" "P" 0 -1 0.0
 "O1P" "OH" 0 -1 0.0
 "O2P" "O2" 0 -1 0.0
 "O3P" "O2" 0 -1 0.0
 "H1P" "HO" 0 -1 0.0
 "C" "C" 0 -1 0.0
 "O" "O" 0 -1 0.0
!entry.Y1P.unit.boundbox array dbl
 -1.00
 0.0
 0.0
 0.0
 0.0
!entry.Y1P.unit.childsequence single int
 2
!entry.Y1P.unit.connect array int
 1
 24
!entry.Y1P.unit.connectivity table  int atom1x  int atom2x  int flags
 1 2 17
 1 3 17
 3 4 17
 3 24 17
 3 5 17
 5 6 17
 5 7 17
 5 8 17
 8 16 17
 8 9 17
 9 10 17
 9 11 17
 11 12 17
 11 13 17
 13 18 17
 13 14 17
 14 15 17
 14 16 17
 16 17 17
 18 19 17
 19 22 17
 19 21 17
 19 20 17
 20 23 17
 24 25 17
!entry.Y1P.unit.hierarchy table  str abovetype  int abovex  str
belowtype  int belowx
 "U" 0 "R" 1
 "R" 1 "A" 1
 "R" 1 "A" 2
 "R" 1 "A" 3
 "R" 1 "A" 4
 "R" 1 "A" 5
 "R" 1 "A" 6
 "R" 1 "A" 7
 "R" 1 "A" 8
 "R" 1 "A" 9
 "R" 1 "A" 10
 "R" 1 "A" 11
 "R" 1 "A" 12
 "R" 1 "A" 13
 "R" 1 "A" 14
 "R" 1 "A" 15
 "R" 1 "A" 16
 "R" 1 "A" 17
 "R" 1 "A" 18
 "R" 1 "A" 19
 "R" 1 "A" 20
 "R" 1 "A" 21
 "R" 1 "A" 22
 "R" 1 "A" 23
 "R" 1 "A" 24
 "R" 1 "A" 25
!entry.Y1P.unit.name single str
 "Y1P"
!entry.Y1P.unit.positions table  dbl x  dbl y  dbl z
 -2.803000 1.247000 -0.295000
 -1.865000 1.556000 -0.174000
 -3.015000 0.022000 -1.037000
 -3.856000 0.168000 -1.70
 -1.782000 -0.305000 -1.915000
 -1.962000 -1.275000 -2.366000
 -1.774000 0.418000 -2.724000
 -0.435000 -0.281000 -1.219000
 0.338000 0.878000 -1.203000
 -0.007000 1.752000 -1.735000
 1.552000 0.94 -0.541000
 2.153000 1.829000 -0.549000
 2.035000 -0.183000 0.121000
 1.299000 -1.362000 0.075000
 1.704000 -2.235000 0.553000
 0.083000 -1.405000 -0.581000
 -0.466000 -2.331000 -0.607000
 3.171000 -0.146000 0.83
 4.653000 0.133000 0.09
 5.55 -0.029000 1.43
 4.676000 1.556000 -0.30
 4.905000 -0.981000 -0.825000
 5.675000 0.835000 1.798000
 -3.448000 -1.169000 -0.177000
 -4.236000 -1.966000 -0.612000
!entry.Y1P.unit.residueconnect table  int c1x  int c2x  int c3x  int
c4x  int c5x  int c6x
 1 24 0 0 0 0
!entry.Y1P.unit.residues table  str name  int seq  int childseq  int
startatomx  str restype  int imagingx
 "Y1P" 1 26 1 "p" 0
!entry.Y1P.unit.residuesPdbSequenceNumber array int
 1
!entry.Y1P.unit.solventcap array dbl
 -1.00
 0.0
 0.0
 0.0
 0.0
!entry.Y1P.unit.velocities table  dbl x  dbl y  dbl z
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0



# Parameters for TYR-PO2(OH) : Y1P; N.Homeyer, A.H.C.Horn, H.Lanig,
H.Sticht, J. Mol. Model., in press
BOND
OS - P   525.0   1.610
OH - P   525.0   1.610

ANGLE
C - OS - P   100.0   120.50
O2 - P - OH  140.0   108.23
HO - OH - P  140.0   108.50
CA - C - OS   70.0   120.00

DIHE

IMPR
CA-CA-C-OS1.1 180.0  2.0


Now, can this be used ...



On Thu, Jun 9, 2011 at 10:30 AM, Dallas Warren wrote:

>  You have been provided there with the reference in which the parameters
> for the molecule were derived.
>
> ** **
>
> Read it!
>
> ** **
>
> And determine yourself if it is applicable or not to what you are doing and
> the 

[gmx-users] Umbrella sampling of phosphate ion binding

[Dallas Warren]

What forcefield is that for?  Sounds like it is more than likely one of the 
AMBER ones.

What forcefield are you using for the rest of your system that you are 
simulating?

Are they the same?  They should be.

If not, are they compatible?  A minor number of them are compatible to some 
degree, such as with a version change for a given forcefield.  However, vast 
majority are not and combining those that aren't compatible them will make a 
nice random number generator that you can spend lots of time using and not get 
anything out that is publishable.

See http://www.gromacs.org/Documentation/Terminology/Force_Fields#Usage and the 
first point at http://www.gromacs.org/Documentation/How-tos/Parameterization

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.
-- 
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!
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Re: [gmx-users] Umbrella sampling of phosphate ion binding

[bharat gupta]

Actually, I am planning to use AMBER forcefield for both phosphotyrosine and
for the system too. The parameters are reliable as they have been published
(http://www.springerlink.com/content/u527364w03568353/fulltext.pdf) . But I
want to know how to add them to the force field. I have checked the
following link :-
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field,
but I want  to do it in a rather shorter way. Like what has been done in the
protein ligand tutorial. But will that be ok to do. As in my case also I too
have a docked complex .

On Wed, Jun 8, 2011 at 10:26 PM, Dallas Warren wrote:

>   What forcefield is that for?  Sounds like it is more than likely one of
> the AMBER ones.
>
> ** **
>
> What forcefield are you using for the rest of your system that you are
> simulating?
>
> ** **
>
> Are they the same?  They should be.
>
> ** **
>
> If not, are they compatible?  A minor number of them are compatible to some
> degree, such as with a version change for a given forcefield.  However, vast
> majority are not and combining those that aren’t compatible them will make a
> nice random number generator that you can spend lots of time using and not
> get anything out that is publishable.
>
> ** **
>
> See http://www.gromacs.org/Documentation/Terminology/Force_Fields#Usageand 
> the first point at
> http://www.gromacs.org/Documentation/How-tos/Parameterization 
>
> ** **
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
>
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail. 
>
> --
> 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
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Why does the -append option exist?

[Roland Schulz]

Hi,

yes that helps a lot. One more question. What filesystem on hopper 2 are you
using for this test (home, scratch or proj, to see if it is Lustre or GPFS)
? And are you running the test on the login node or on the compute node?

Thanks
Roland

On Wed, Jun 8, 2011 at 1:17 PM, Dimitar Pachov  wrote:

> Hello,
>
> On Wed, Jun 8, 2011 at 4:21 AM, Sander Pronk  wrote:
>
>> Hi Dimitar,
>>
>> Thanks for the bug report. Would you mind trying the test program I
>> attached on the same file system that you get the truncated files on?
>>
>> compile it with gcc testje.c -o testio
>>
>
> Yes, but no problem:
>
> 
> [dpachov@login-0-0 NEWTEST]$ ./testio
> TEST PASSED: ftell gives: 46
> 
>
> As for the other questions:
>
> HPC OS version:
> 
> [dpachov@login-0-0 NEWTEST]$ uname -a
> Linux login-0-0.local 2.6.18-194.17.1.el5xen #1 SMP Mon Sep 20 07:20:39 EDT
> 2010 x86_64 x86_64 x86_64 GNU/Linux
> [dpachov@login-0-0 NEWTEST]$ cat /etc/redhat-release
> Red Hat Enterprise Linux Server release 5.2 (Tikanga)
> 
>
> GROMACS 4.5.4 built:
> 
> module purge
> module load INTEL/intel-12.0
> module load OPENMPI/1.4.3_INTEL_12.0
> module load FFTW/2.1.5-INTEL_12.0 # not needed
>
> #
> # GROMACS settings
>
> export CC=mpicc
> export F77=mpif77
> export CXX=mpic++
> export FC=mpif90
> export F90=mpif90
>
> make distclean
>
> echo "XXX building single prec XX"
>
> ./configure
> --prefix=/home/dpachov/mymodules/GROMACS/EXEC/4.5.4-INTEL_12.0/SINGLE \
> --enable-mpi \
>  --enable-shared \
> --program-prefix="" --program-suffix="" \
> --enable-float --disable-fortran \
> --with-fft=mkl \
> --with-external-blas \
> --with-external-lapack \
> --with-gsl \
> --without-x \
> CFLAGS="-O3 -funroll-all-loops" \
> FFLAGS="-O3 -funroll-all-loops" \
> CPPFLAGS="-I${MPI_INCLUDE} -I${MKL_INCLUDE} " \
> LDFLAGS="-L${MPI_LIB} -L${MKL_LIB} -lmkl_intel_lp64 -lmkl_core
> -lmkl_intel_thread -liomp5 "
>
> make -j 8 && make install
> 
>
> Just did the same test on Hopper 2:
> http://www.nersc.gov/users/computational-systems/hopper/
>
> with their built GROMACS 4.5.3 (gromacs/4.5.3(default)), and the result was
> the same as reported earlier. You could do the test there as well, if you
> have access, and see what you would get.
>
> Hope that helps a bit.
>
> Thanks,
> Dimitar
>
>
>
>
>
>>
>> Sander
>>
>>
>>
>>
>>
>> On Jun 7, 2011, at 23:21 , Dimitar Pachov wrote:
>>
>> Hello,
>>
>> Just a quick update after a few shorts tests we (my colleague and I)
>> quickly did. First, using
>>
>> "*You can emulate this yourself by calling "sleep 10s" before mdrun and
>> see if that's long enough to solve the latency issue in your case.*"
>>
>> doesn't work for a few reasons, mainly because it doesn't seem to be a
>> latency issue, but also because the load on a node is not affected by
>> "sleep".
>>
>> However, you can reproduce the behavior I have observed pretty easily. It
>> seems to be related to the values of the pointers to the *xtc, *trr, *edr,
>> etc files written at the end of the checkpoint file after abrupt crashes AND
>> to the frequency of access (opening) to those files. How to test:
>>
>> 1. In your input *mdp file put a high frequency of saving coordinates to,
>> say, the *xtc (10, for example) and a low frequency for the *trr file
>> (10,000, for example).
>> 2. Run GROMACS (mdrun -s run.tpr -v -cpi -deffnm run)
>> 3. Kill abruptly the run shortly after that (say, after 10-100 steps).
>> 4. You should have a few frames written in the *xtc file, and the only one
>> (the first) in the *trr file. The *cpt file should have different from zero
>> values for "file_offset_low" for all of these files (the pointers have been
>> updated).
>>
>> 5. Restart GROMACS (mdrun -s run.tpr -v -cpi -deffnm run).
>> 6. Kill abruptly the run shortly after that (say, after 10-100 steps). Pay
>> attention that the frequency for accessing/writing the *trr has not been
>> reached.
>> 7. You should have a few additional frames written in the *xtc file, while
>> the *trr will still have only 1 frame (the first). The *cpt file now has
>> updated all pointer values "file_offset_low", BUT the pointer to the *trr
>> has acquired a value of 0. Obviously, we already now what will happen if we
>> restart again from this last *cpt file.
>>
>> 8. Restart GROMACS (mdrun -s run.tpr -v -cpi -deffnm run).
>> 9. Kill it.
>> 10. File *trr has size zero.
>>
>>
>> Therefore, if a run is killed before the files are accessed for writing
>> (depending on the chosen frequency), the file offset values reported in the
>> *cpt file doesn't seem to be accordingly updated, and hence a new restart
>> inevitably leads to overwritten output files.
>>
>> Do you think this is fixable?
>>
>> Thanks,
>> Dimitar
>>
>>
>>
>>
>>
>>
>> On Sun, Jun 5, 2011 at 6:20 PM, Roland Schulz  wrote:
>>
>>> Two comments about the discussion:
>>>
>>> 1) I agree that buffered output (Kernel buffers - not application
>>> buffers) should not affect I/O. If it does it should be filed as bug to the