Re: [gmx-users] Vizualization with VMD: no image appears

[rama david]

Dear,
   -o MT.PnoH.xtc instad of xtc extenstion use pdb you will get pdb file.
And then load it in vmd or pymol u can see it

On Wed, Nov 21, 2012 at 10:24 PM, Rausch, Felix wrote:

> Hi.
>
> Try to load in a .gro file of your system first. After that, use the "load
> data into molecule" option to load in the .xtc.
>
> -Ursprüngliche Nachricht-
> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> Im Auftrag von shch406
> Gesendet: Mittwoch, 21. November 2012 17:47
> An: gmx-users@gromacs.org
> Betreff: [gmx-users] Vizualization with VMD: no image appears
>
> Dear Gromacs users
>
> To visualize my trajectory with VMD I applied trjconv to .xtc trajectory
> file to eliminate water molecules and velocities remaining protein
> coordinates only.
> However, when I load this reduced file to VMD no image on screen appears,
> nevertheless VMD have identified the file as a "Gromacs compress trajectory
> file".
> What may be the cause of this?
>
> The corresponding command is as follows:
>
> trjconv -f MT.xtc -o MT.PnoH.xtc skip 1 -n defau.ndx -pbc nojump -novel
>
> where MT.xtc contains ~10 frames, defau.ndx is default groups index file.
> Group 2 (Protein-H) was chosen handling dialog.
>
> Merci pour votre collaboration,
> Igor Shchechkin
>
>
>
>
> --
> View this message in context:
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> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] RE: GROMACS96 proper dihetral parameters/OPLS

[Justin Lemkul]

On 11/21/12 9:56 PM, junfang.zh...@csiro.au wrote:

Dear GROMACS users

I am just wondering if you could help with transferring the GROMACS96 proper 
dihetral parameters to the OPLS proper dihedral parameters or point me to some 
references.



Gromos96 uses periodic dihedrals and OPLS uses Ryckaert-Bellemans.  The forms of 
these two are very different and it isn't clear to me how the two would be 
interconverted.  If you want to use OPLS and the dihedral isn't defined, derive 
it in a manner consistent with the original force field.  Trying to transfer 
different parameters between force fields probably isn't worth the effort.



GROMACS96 dihedral:


OPLS dihedral:


My second question is if CO2 has been parameterised in GROMACS96 force field.



Maybe, but note that no such force field exists.  Your literature searching will 
probably be more fruitful if you use correct terminology (Gromos96), which has a 
number of parameter sets that have been developed over the years.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Gromacs GPU

[Justin Lemkul]

Can you re-compile with debugging symbols and obtain a full backtrace?

-Justin

On 11/21/12 11:58 AM, Emanuele Coccia wrote:

4.1.1 installed from binaries.

2012/11/21 Justin Lemkul 




On 11/21/12 11:11 AM, Emanuele Coccia wrote:


Running your benchmark for the first time (dhfr-impl-1nm.bench) I have the
following message:


*Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single
precision)
*
*
*
*WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.*
*
*
*
*
*WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek integrators.*
*
*
*
*
*WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and

CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
option.*
*
*
*
*
*WARNING: The OBC scale factors alpha, beta and gamma are hardcoded in
OpenMM with the default Gromacs values.*
*
*
*Floating point exception*
*
*
*

*
The floating point exception could be due to some other error, I'd be sure
that it doesn't depend on the GPU card.



In theory, the newer card should be fine.  What version of OpenMM are you
using?


-Justin

--
==**==

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Department of Biochemistry
Virginia Tech
Blacksburg, VA
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[gmx-users] RE: GROMACS96 proper dihetral parameters/OPLS

[Junfang.Zhang]

Dear GROMACS users

I am just wondering if you could help with transferring the GROMACS96 proper 
dihetral parameters to the OPLS proper dihedral parameters or point me to some 
references.

GROMACS96 dihedral:


OPLS dihedral:


My second question is if CO2 has been parameterised in GROMACS96 force field.


Thank you in advance

Junfang


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Re: [gmx-users] how to repeat simulation correctly?

[Mark Abraham]

Generating velocities from a new random seed is normally regarded as good
enough. By the time you equilibrate, the chaotic nature of MD starts to
work for you.

Mark
On Nov 21, 2012 1:04 PM, "Felipe Pineda, PhD" 
wrote:

> So how would you repeat the (let be it converged) simulation from
> different starting conditions in order to add that valuable statistics you
> mention?
>
> I think this was Albert's question
>
> Felipe
>
> On 11/21/2012 12:41 PM, Mark Abraham wrote:
>
>> If a simulation ensemble doesn't converge reliably over a given time
>> scale,
>> then it's not converged over that time scale. Repeating it from different
>> starting conditions still adds valuable statistics, but can't be a
>> replicate. Independent replicated observations of the same phenomenon
>> allow
>> you to assess how likely it is that your set of observations reflect the
>> underlying phenomenon. The problem in sampling-dependent MD is usually in
>> making an observation (equating a converged simulation with an
>> observation).
>>
>> Mark
>>
>> On Wed, Nov 21, 2012 at 8:12 AM, Albert  wrote:
>>
>>  hello:
>>>
>>>I am quite confused on how to repeat our MD in Gromacs. If we started
>>> from the same equilibrated .gro file with "gen_vel= no" in
>>> md.mdp,
>>> we may get "exactly" the same results which cannot be treated as
>>> reasonable
>>> repeated running. However, if we use "gen_vel=yes" for each round of
>>> running, sometimes our simulation may not converged at our simulated time
>>> scale and we may get two results with large differences.
>>>
>>>So I am just wondering how to perform repeated MD in Gromacs in a
>>> correct way so that our results can be acceptably repeated?
>>>
>>> thank you very much.
>>> Albert
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
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>>> >
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>>> 
>>> >
>>>
>>>
>
> --
> +-**--+
> | Luis Felipe Pineda De Castro, PhD |
> | Computational Chemist - Postdoc   |
> | Computational Chemistry and   |
> | Biochemistry Laboratory   |
> | School of Natural Sciences|
> | Linnaeus University   |
> | SE-391 82 Kalmar  |
> | Norrgård, room 311|
> | Sweden - Sverige  |
> | Phone:  ++46-480-44 6329  |
> | Mobile: ++46-76-8420572   |
> | E-Mail: luis.pinedadecas...@lnu.se|
> | Web:lnu.se|
> +-**--+
>
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Re: [gmx-users] Gromacs 4.6 segmentation fault with mdrun

[Szilárd Páll]

Roland,

He explicitly stated that he is using 20da718 which is also from the
nbnxn_hybrid_acc branch.

Raf, as Roland said, get the release-4-6 ad try again!


There's an important thing to mention: your hardware configuration is
probably quite imbalanced and the default settings are certainly not the
best to run with: two MPI processes/threads with 24 OpenMP threads + a GPU
each. GROMACS works best with balanced hardware configuration and yours is
certainly not balanced, the GPUs will not be able to keep up with 64 CPU
cores.

Regarding the run configuration  most importantly, in most cases you should
avoid running a group of OpenMP threads across sockets (except on Intel,
<=12-16 threads). On these Opterons  running OpenMP at most on a half CPU
is recommended (the CPUs are in reality two CPU dies bolted together) and
in fact you might be better off with even less threads per MPI
process/thread. This means that multiple processes will have to share a GPU
which is not optimal and work only with MPI in the current version.

So to conclude, to get the best performance you should try a few
combinations:

# process 0,1 will use GPU0, process 2,3 GPU1
# this avoids running across sockets, but for aforementioned reasons it
will still be suboptimal
mpirun -np 4 mdrun_mpi -gpu_id 0011

# process 0,1,2,3 will use GPU0, process 4,5,6,7 GPU1
# this config will probably still be slower than the next one
mpirun -np 8 mdrun_mpi -gpu_id 1

# process 0,1,2,3,4,5,6,7 will use GPU0, process 8,9,10,11,12,13,14,15 GPU1
# this config will probably still be slower than the next one
mpirun -np 16 mdrun_mpi -gpu_id 1

You should go ahead and try with 32 and 64 processes as well, I suspect
that 2 or 3 threads/process will be the fastest. Depending on what system
you are simulating, this could lead to load imbalance, but that you'll have
to see.

If it turns out that the "Wait for GPU" time is more than a few percent
(which will probably be the case), it means that a GTX 580 is not fast
enough for two of these Opterons. What you can try is to run using the
"hybrid" mode with "-nb gpu_cpu" which might help.

Cheers,

--
Szilárd


On Sat, Nov 17, 2012 at 3:11 AM, Roland Schulz  wrote:

> Hi Raf,
>
> which version of Gromacs did you use? If you used branch nbnxn_hybrid_acc
> please use branch release-4-6 instead and see whether that fixes your
> issue. If not please open a bug and upload your log file and your tpr.
>
> Roland
>
>
> On Thu, Nov 15, 2012 at 5:13 PM, Raf Ponsaerts <
> raf.ponsae...@med.kuleuven.be> wrote:
>
> > Hi Szilárd,
> >
> > I assume I get the same segmentation fault error as Sebastian (don't
> > shoot if not so). I have 2 NVIDA GTX580 cards (and 4x12-core amd64
> > opteron 6174).
> >
> > in brief :
> > Program received signal SIGSEGV, Segmentation fault.
> > [Switching to Thread 0x7fffc07f8700 (LWP 32035)]
> > 0x761de301 in nbnxn_make_pairlist.omp_fn.2 ()
> > from /usr/local/gromacs/bin/../lib/libmd.so.6
> >
> > Also -nb cpu with Verlet cutoff-scheme results in this error...
> >
> > gcc 4.4.5 (Debian 4.4.5-8), Linux kernel 3.1.1
> > CMake 2.8.7
> >
> > If I attach the mdrun.debug output file to this mail, the mail to the
> > list gets bounced by the mailserver (because mdrun.debug > 50 Kb).
> >
> > Hoping this might help,
> >
> > regards,
> >
> > raf
> > ===
> > compiled code :
> > commit 20da7188b18722adcd53088ec30e5f256af62f20
> > Author: Szilard Pall 
> > Date:   Tue Oct 2 00:29:33 2012 +0200
> >
> > ===
> > (gdb) exec mdrun
> > (gdb) run -debug 1 -v -s test.tpr
> >
> > Reading file test.tpr, VERSION 4.6-dev-20121002-20da718 (single
> > precision)
> > [New Thread 0x73844700 (LWP 31986)]
> > [Thread 0x73844700 (LWP 31986) exited]
> > [New Thread 0x73844700 (LWP 31987)]
> > [Thread 0x73844700 (LWP 31987) exited]
> > Changing nstlist from 10 to 50, rlist from 2 to 2.156
> >
> > Starting 2 tMPI threads
> > [New Thread 0x73844700 (LWP 31992)]
> > Using 2 MPI threads
> > Using 24 OpenMP threads per tMPI thread
> >
> > 2 GPUs detected:
> >   #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat:
> > compatible
> >   #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat:
> > compatible
> >
> > 2 GPUs auto-selected to be used for this run: #0, #1
> >
> >
> > Back Off! I just backed up ctab14.xvg to ./#ctab14.xvg.1#
> > Initialized GPU ID #1: GeForce GTX 580
> > [New Thread 0x73043700 (LWP 31993)]
> >
> > Back Off! I just backed up dtab14.xvg to ./#dtab14.xvg.1#
> >
> > Back Off! I just backed up rtab14.xvg to ./#rtab14.xvg.1#
> > [New Thread 0x71b3c700 (LWP 31995)]
> > [New Thread 0x7133b700 (LWP 31996)]
> > [New Thread 0x70b3a700 (LWP 31997)]
> > [New Thread 0x7fffebfff700 (LWP 31998)]
> > [New Thread 0x7fffeb7fe700 (LWP 31999)]
> > [New Thread 0x7fffeaffd700 (LWP 32000)]
> > [New Thread 0x7fffea7fc700 (LWP 32001)]
> > [New Thread 0x7fffe9ffb700 (LWP 32002)]
> > [New Thread 0x7fffe97fa700 (LWP 32003)]
> > [New Thread 0x

Re: [gmx-users] GPU warnings

[Szilárd Páll]

On Mon, Nov 19, 2012 at 6:25 PM, Szilárd Páll wrote:

> On Mon, Nov 19, 2012 at 4:09 PM, Thomas Evangelidis wrote:
>
>> Hi Szilárd,
>>
>> I compiled with the Intel compilers, not gcc. In case I am missing
>> something, these are the versions I have:
>>
>
> Indeed, I see it now in the log file. Let me try with icc 13 and will get
> back to you.
>

I was able to run code compiled with icc 13 on Fedora 17, but as I don't
have Intel Compiler v13 on this machine I can't check it now.

Please check if it works for you with gcc 4.7.2 (which is the default) and
let me know if you succeed. The performance difference between icc and gcc
on your processor should be negligible with GPU runs and at most 5-10% with
CPU-only runs.

As the issue is quite annoying, I'll try to have a look later, probably
after the beta is out.

Cheers,
Sz.


>
>> glibc.i6862.15-57.fc17
>> @updates
>> glibc.x86_64  2.15-57.fc17
>> @updates
>> glibc-common.x86_64   2.15-57.fc17
>> @updates
>> glibc-devel.i686  2.15-57.fc17
>> @updates
>> glibc-devel.x86_642.15-57.fc17
>> @updates
>> glibc-headers.x86_64  2.15-57.fc17   @updates
>>
>> gcc.x86_644.7.2-2.fc17
>> @updates
>> gcc-c++.x86_644.7.2-2.fc17
>> @updates
>> gcc-gfortran.x86_64   4.7.2-2.fc17
>> @updates
>> libgcc.i686   4.7.2-2.fc17
>> @updates
>> libgcc.x86_64 4.7.2-2.fc17   @updates
>>
>>
>> Thomas
>>
>>
>>
>> On 19 November 2012 16:57, Szilárd Páll  wrote:
>>
>> > Thomas & Albert,
>> >
>> > We are unable to reproduce the issue on FC 17 with glibc 2.15-58 and gcc
>> > 4.7.2.
>> >
>> > Please try to update your packages (you should have updates available
>> for
>> > glibc), try recompiling with the latest 4.6 code and report back whether
>> > you succeed.
>> >
>> > Cheers,
>> >
>> > --
>> > Szilárd
>> >
>> >
>> > On Fri, Nov 16, 2012 at 4:31 PM, Szilárd Páll > > >wrote:
>> >
>> > > Hi Albert,
>> > >
>> > > Apologies for hijacking your thread. Do you happen to have Fedora 17
>> as
>> > > well?
>> > >
>> > > --
>> > > Szilárd
>> > >
>> > >
>> > >
>> > > On Sun, Nov 4, 2012 at 10:55 AM, Albert  wrote:
>> > >
>> > >> hello:
>> > >>
>> > >>  I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti
>> (2 x
>> > >> 1344 CUDA cores), and I got the following warnings:
>> > >>
>> > >> thank you very much.
>> > >>
>> > >> ---**messages--**
>> > >> -
>> > >>
>> > >> WARNING: On node 0: oversubscribing the available 0 logical CPU cores
>> > per
>> > >> node with 2 MPI processes.
>> > >>  This will cause considerable performance loss!
>> > >>
>> > >> 2 GPUs detected on host boreas:
>> > >>   #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>> > >> compatible
>> > >>   #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
>> > >> compatible
>> > >>
>> > >> 2 GPUs auto-selected to be used for this run: #0, #1
>> > >>
>> > >> Using CUDA 8x8x8 non-bonded kernels
>> > >> Making 1D domain decomposition 1 x 2 x 1
>> > >>
>> > >> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
>> > >> We have just committed the new CPU detection code in this branch,
>> > >> and will commit new SSE/AVX kernels in a few days. However, this
>> > >> means that currently only the NxN kernels are accelerated!
>> > >> In the mean time, you might want to avoid production runs in 4.6.
>> > >>
>> > >> --
>> > >> gmx-users mailing listgmx-users@gromacs.org
>> > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> > >> * Please search the archive at http://www.gromacs.org/**
>> > >> Support/Mailing_Lists/Search<
>> > 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<
>> > http://www.gromacs.org/Support/Mailing_Lists>
>> > >>
>> > >
>> > >
>> > --
>> > gmx-users mailing listgmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > * Please search the archive at
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>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>>
>>
>>
>> --
>>
>> ==
>>
>> Thomas Evangelidis
>>
>> PhD student
>> University of Athens
>> Faculty of Pharmacy
>> Department of Pharmaceutical Chemistry
>> Panepistimioupoli-Zografou
>> 157 71 Athens
>> GREECE
>>
>> email: tev...@pharm.uo

[gmx-users] g_select

[akn]

Dear All, 

I'd like to calculate the profile of a physical properties.
I used g_select command as below.
The value of i can be increased by an integer value. For example, the
command in the below
the z axis of the cell is divided the bins by the tickness of 2 nm. However
I'd make the tickness of each bin 0.2 nm.
How can I do that? Please can you answer me?

groups=`grep "^\[" index.ndx | wc -l`
j=0;
for ((i=120; i<=124; i=i+2)); do
j=$(($j+1));

g_select -f traj.xtc -s topol.tpr -n index.ndx -on selectNZ1_$j.ndx -select
'"Hbond" z '$i' to '$(($i+2))'  and name NZ' ;
done

thanks,

Akn.



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[gmx-users] REMD with umbrella sampling in Gromacs 4.5.5

[dejun_...@urmc.rochester.edu]

Hi all,

I've read some earlier posts in the forum about replica exchange combined
with umbrella sampling but still not sure if the restrain potential defined
in the pull code will be included in the exchange criterion:

P(i<->j) = min (1, exp[ (beta_i-beta_j)*(U(Ri, Dj) + U(Rj,Di) - U(Ri,Di) -
U(Rj,Dj)) ] where i, j are 2 replica and beta, R, D are the respective
inverse temperature, Cartesian coordinates and parameters in the pull code
(force constant, equilibrium position etc.). 

Can anyone clarify that? 

Thanks,
Dejun



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[gmx-users] REMD with umbrella sampling in Gromacs 4.5.5

[Lin, Dejun]

Hi all, 

I've read some earlier posts in the forum about replica exchange combined with 
umbrella sampling but still not sure if the restrain potential defined in the 
pull code will be included in the exchange criterion: 

P(i<->j) = min (1, exp[ (beta_i-beta_j)*(U(Ri, Dj) + U(Rj,Di) - U(Ri,Di) - 
U(Rj,Dj)) ] where i, j are 2 replica and beta, R, D are the respective inverse 
temperature, Cartesian coordinates and parameters in the pull code (force 
constant, equilibrium position etc.). 

Can anyone clarify that? 

Thanks, 
Dejun--
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Re: [gmx-users] Gromacs GPU

[Emanuele Coccia]

4.1.1 installed from binaries.

2012/11/21 Justin Lemkul 

>
>
> On 11/21/12 11:11 AM, Emanuele Coccia wrote:
>
>> Running your benchmark for the first time (dhfr-impl-1nm.bench) I have the
>> following message:
>>
>>
>> *Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single
>> precision)
>> *
>> *
>> *
>> *WARNING: OpenMM does not support leap-frog, will use velocity-verlet
>> integrator.*
>> *
>> *
>> *
>> *
>> *WARNING: OpenMM supports only Andersen thermostat with the
>> md/md-vv/md-vv-avek integrators.*
>> *
>> *
>> *
>> *
>> *WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
>>
>> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
>> option.*
>> *
>> *
>> *
>> *
>> *WARNING: The OBC scale factors alpha, beta and gamma are hardcoded in
>> OpenMM with the default Gromacs values.*
>> *
>> *
>> *Floating point exception*
>> *
>> *
>> *
>>
>> *
>> The floating point exception could be due to some other error, I'd be sure
>> that it doesn't depend on the GPU card.
>>
>>
> In theory, the newer card should be fine.  What version of OpenMM are you
> using?
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
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>



-- 
Emanuele

Università degli Studi dell'Aquila
Dipartimento di Chimica, Ingegneria Chimica e Materiali
CBBC Group - http://bio.phys.uniroma1.it
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AW: [gmx-users] Vizualization with VMD: no image appears

[Rausch, Felix]

Hi. 

Try to load in a .gro file of your system first. After that, use the "load data 
into molecule" option to load in the .xtc.

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von shch406
Gesendet: Mittwoch, 21. November 2012 17:47
An: gmx-users@gromacs.org
Betreff: [gmx-users] Vizualization with VMD: no image appears

Dear Gromacs users

To visualize my trajectory with VMD I applied trjconv to .xtc trajectory file 
to eliminate water molecules and velocities remaining protein coordinates only.
However, when I load this reduced file to VMD no image on screen appears, 
nevertheless VMD have identified the file as a "Gromacs compress trajectory 
file".
What may be the cause of this?

The corresponding command is as follows:

trjconv -f MT.xtc -o MT.PnoH.xtc skip 1 -n defau.ndx -pbc nojump -novel

where MT.xtc contains ~10 frames, defau.ndx is default groups index file.
Group 2 (Protein-H) was chosen handling dialog.

Merci pour votre collaboration,
Igor Shchechkin




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Re: [gmx-users] Vizualization with VMD: no image appears

[Justin Lemkul]

On 11/21/12 11:45 AM, shch406 wrote:

Dear Gromacs users

To visualize my trajectory with VMD I applied trjconv to .xtc trajectory
file to eliminate water molecules and velocities remaining protein
coordinates only.
However, when I load this reduced file to VMD no image on screen appears,
nevertheless VMD have identified the file as a "Gromacs compress trajectory
file".
What may be the cause of this?



You need to load a matching coordinate file (.pdb, .gro, etc) first and then 
load the trajectory as data for it.  The contents of the coordinate file and 
.xtc must match; if there is a different number of coordinates in each, then VMD 
will fail to load the trajectory properly.


-Justin


The corresponding command is as follows:

trjconv -f MT.xtc -o MT.PnoH.xtc skip 1 -n defau.ndx -pbc nojump -novel

where MT.xtc contains ~10 frames, defau.ndx is default groups index file.
Group 2 (Protein-H) was chosen handling dialog.

Merci pour votre collaboration,
Igor Shchechkin




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--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Gromacs GPU

[Justin Lemkul]

On 11/21/12 11:11 AM, Emanuele Coccia wrote:

Running your benchmark for the first time (dhfr-impl-1nm.bench) I have the
following message:


*Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision)
*
*
*
*WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.*
*
*
*
*
*WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek integrators.*
*
*
*
*
*WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
option.*
*
*
*
*
*WARNING: The OBC scale factors alpha, beta and gamma are hardcoded in
OpenMM with the default Gromacs values.*
*
*
*Floating point exception*
*
*
*
*
The floating point exception could be due to some other error, I'd be sure
that it doesn't depend on the GPU card.



In theory, the newer card should be fine.  What version of OpenMM are you using?

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Vizualization with VMD: no image appears

[shch406]

Dear Gromacs users

To visualize my trajectory with VMD I applied trjconv to .xtc trajectory
file to eliminate water molecules and velocities remaining protein
coordinates only.
However, when I load this reduced file to VMD no image on screen appears,
nevertheless VMD have identified the file as a "Gromacs compress trajectory
file".
What may be the cause of this?

The corresponding command is as follows:

trjconv -f MT.xtc -o MT.PnoH.xtc skip 1 -n defau.ndx -pbc nojump -novel

where MT.xtc contains ~10 frames, defau.ndx is default groups index file.
Group 2 (Protein-H) was chosen handling dialog.

Merci pour votre collaboration,
Igor Shchechkin




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Re: [gmx-users] Gromacs GPU

[Emanuele Coccia]

Running your benchmark for the first time (dhfr-impl-1nm.bench) I have the
following message:


*Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision)
*
*
*
*WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.*
*
*
*
*
*WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek integrators.*
*
*
*
*
*WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
option.*
*
*
*
*
*WARNING: The OBC scale factors alpha, beta and gamma are hardcoded in
OpenMM with the default Gromacs values.*
*
*
*Floating point exception*
*
*
*
*
The floating point exception could be due to some other error, I'd be sure
that it doesn't depend on the GPU card.

Thank you


2012/11/21 Justin Lemkul 

>
>
> On 11/21/12 10:43 AM, Emanuele Coccia wrote:
>
>> Dear Support,
>>
>>   I have installed the version 4.5.5 of Gromacs, I have also installede
>> mdrun-gpu. I have a GeForce GTX 670 and CUDA toolkit 4.0; is this
>> environment compatible with Gromacs-GPU?
>>
>>
> Likely.  Are you having some issue getting mdrun to work?  Note that the
> hardware/software compatibility list on the website (and even within the
> code) is outdated, so newer cards like these should work.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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> Support/Mailing_Lists/Searchbefore
>  posting!
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> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
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>



-- 
Emanuele

Università degli Studi dell'Aquila
Dipartimento di Chimica, Ingegneria Chimica e Materiali
CBBC Group - http://bio.phys.uniroma1.it
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Re: [gmx-users] Gromacs GPU

[Justin Lemkul]

On 11/21/12 10:43 AM, Emanuele Coccia wrote:

Dear Support,

  I have installed the version 4.5.5 of Gromacs, I have also installede
mdrun-gpu. I have a GeForce GTX 670 and CUDA toolkit 4.0; is this
environment compatible with Gromacs-GPU?



Likely.  Are you having some issue getting mdrun to work?  Note that the 
hardware/software compatibility list on the website (and even within the code) 
is outdated, so newer cards like these should work.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Re: hpo4

[Justin Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private Gromacs tutor.


On 11/21/12 9:50 AM, Kdead wrote:

Hello,
I have another problem after change the parameters.In the 43a1 force
fieldga_13  is 109.6 °，but my
ga_13 <90 °  after  mdrun by Pymol software。 why？ thank you very much！！


I don't know, aside from suspecting something else is wrong with the topology. 
The equilibrium value of the angle should be pretty well maintained during the 
simulation, with only slight deviations.  If you have some larger collapse of 
the structure, something else about the topology is unstable.  Again, mapping 
everything back to a known entity like ATP is an appropriate course of action.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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AW: [gmx-users] pressure_coupling

[Florian Dommert]

---
Florian Dommert
Dipl. Phys.

Institut für Computerphysik
Universität Stuttgart
Allmandring 3
D-70569 Stuttgart

Tel.: 0711-68563613
Fax: 0711-68563658


> -Ursprüngliche Nachricht-
> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] Im Auftrag von tarak karmakar
> Gesendet: Mittwoch, 21. November 2012 15:03
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] pressure_coupling
> 
> Thanks for the information Flo.
> Before doing NPT I have already equilibrated my system by heating it from
0K to
> 300K in 300 ps, then the pressure has reached to 1 bar. Now while doing
NPT I'm
> getting the excess pressure.
> Is there any problem with the coupling constant ? I am checking it by
taking
> different tau_p values. Let's see.
> 

I don't think that playing around with the coupling constant will help you.
You can set it to extreme values, but you won't see any difference. The
coupling constant determines, how fast the system pressure should relax to
the reference pressure. I would see a better possibility to play around by
simulating for a longer time. Then observing the variation of the pressure
in time, the size of the fluctuation and the excess pressure. Perhaps
something will change, but I don't think so. I play around with the coupling
constants but observed no change.

Maybe, but this is really speculation, there is a problem with the
combination of constraints and MTTK. Please check the archives of the user
and developer list to obtain more information.

/Flo

> 
> On Wed, Nov 21, 2012 at 1:16 AM, Florian Dommert  stuttgart.de> wrote:
> >> -Ursprüngliche Nachricht-
> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> >> boun...@gromacs.org] Im Auftrag von Justin Lemkul
> >> Gesendet: Dienstag, 20. November 2012 18:33
> >> An: Discussion list for GROMACS users
> >> Betreff: Re: [gmx-users] pressure_coupling
> >>
> >>
> >>
> >> On 11/20/12 12:29 PM, tarak karmakar wrote:
> >> > Thanks Justin for the quick reply.
> >> > Is there any problem with the algorithms ??
> >> >
> >> > I have used Velocity Verlet , Nose-Hoover and MTTK combination.
> >> > SHAKE has been used to constrains the H-covalent bonds.
> >> > tau_t = 1 ps
> >> > tau_P = 1 ps
> >> > I got the mean pressure at ~130 bar.
> >> >
> >> > Previously with the same initial coordinates I have used Leap-Frog,
> >> > NH, Parinello-Rehman with LINCS to constrain H-covalent bonds.
> >> > tau_t was 0.1 ps
> >> > and tau P was 2 ps.
> >> > The I have seen the pressure fluctuating around 1 bar( as expected)
> >> > So can you please inform me from where this problem is coming -
> >> > algorithms and/ tau_t and tau_P parameters ?
> >> >
> >>
> >> I have no personal experience with the md-vv/MTTK combination.  The
> >> way to test if there is a bug or something is to take an equilibrated
> >> system (as
> > suggested
> >> before) and continue it with the desired parameters.  If they deviate
> >> or incorrectly report pressure, then there's probably a bug.  I'm not
> >> ready
> > to
> >> conclude that until it is tested though.
> >>
> >> -Justin
> >>
> >
> > I once tried to use the same combination of T and P coupling and MD-vv
> > for a system, which could be simulated with PR at 1bar without
> > problems. But I also observed this large pressure. Somehow I have in
> > mind, that there was recently a thread about MTTK coupling on the list
> > with the conclusion that MTTK is so far not stable, but please check the
> archives to assure this.
> >
> > /Flo
> >
> >> > On Tue, Nov 20, 2012 at 10:10 PM, Justin Lemkul 
> wrote:
> >> >>
> >> >>
> >> >> On 11/20/12 11:26 AM, tarak karmakar wrote:
> >> >>>
> >> >>> Dear All,
> >> >>>
> >> >>> I want to keep the pressure at 1.0 bar during the NPT simulation.
> >> >>> But it is fluctuating around 130 bar. So can anyone please inform
> >> >>> me whether I have missed any keyword in my .mdp file OR is it
> >> >>> because of the tau_p which I set 1s 1.0 ps.
> >> >>
> >> >>
> >> >> Equilibrate with a weak coupling method (Berendsen) and then
> >> >> proceed using better algorithms.
> >> >>
> >> >> -Justin
> >> >>
> >> >>
> >> >>> Thanks
> >> >>>
> >> >>> The .mdp file is given below
> >> >>>
> >> >>>
> >> >>>
> >> >>> ; 7.3.3 Run Control
> >> >>> integrator  = md-vv; md integrator
> >> >>> tinit   = 0 ; [ps] starting
time
> > for
> >> >>> run
> >> >>> dt  = 0.001 ; [ps] time step
for
> >> >>> integration
> >> >>> nsteps  = 1500; maximum number
of
> >> >>> steps to integrate, 0.001 * 15,00,000 = 15 ns
> >> >>> nstcomm = 1 ; [steps] frequency
of
> >> >>> mass motion removal
> >> >>> comm_grps   = Protein Non-Protein   ; group(s) for
center
> >> >>> of mass motion removal
> >> >>>
> >> >>> ; 7.3.8 Output Control
> >> >>> nstxout = 1; [steps] freq to

Re: [gmx-users] pressure_coupling

[tarak karmakar]

Thanks for the information Flo.
Before doing NPT I have already equilibrated my system by heating it
from 0K to 300K in 300 ps, then the pressure has reached to 1 bar. Now
while doing NPT I'm getting the excess pressure.
Is there any problem with the coupling constant ? I am checking it by
taking different tau_p values. Let's see.


On Wed, Nov 21, 2012 at 1:16 AM, Florian Dommert
 wrote:
>> -Ursprüngliche Nachricht-
>> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
>> boun...@gromacs.org] Im Auftrag von Justin Lemkul
>> Gesendet: Dienstag, 20. November 2012 18:33
>> An: Discussion list for GROMACS users
>> Betreff: Re: [gmx-users] pressure_coupling
>>
>>
>>
>> On 11/20/12 12:29 PM, tarak karmakar wrote:
>> > Thanks Justin for the quick reply.
>> > Is there any problem with the algorithms ??
>> >
>> > I have used Velocity Verlet , Nose-Hoover and MTTK combination. SHAKE
>> > has been used to constrains the H-covalent bonds.
>> > tau_t = 1 ps
>> > tau_P = 1 ps
>> > I got the mean pressure at ~130 bar.
>> >
>> > Previously with the same initial coordinates I have used Leap-Frog,
>> > NH, Parinello-Rehman with LINCS to constrain H-covalent bonds.
>> > tau_t was 0.1 ps
>> > and tau P was 2 ps.
>> > The I have seen the pressure fluctuating around 1 bar( as expected) So
>> > can you please inform me from where this problem is coming -
>> > algorithms and/ tau_t and tau_P parameters ?
>> >
>>
>> I have no personal experience with the md-vv/MTTK combination.  The way to
>> test if there is a bug or something is to take an equilibrated system (as
> suggested
>> before) and continue it with the desired parameters.  If they deviate or
>> incorrectly report pressure, then there's probably a bug.  I'm not ready
> to
>> conclude that until it is tested though.
>>
>> -Justin
>>
>
> I once tried to use the same combination of T and P coupling and MD-vv for a
> system, which could be simulated with PR at 1bar without problems. But I
> also observed this large pressure. Somehow I have in mind, that there was
> recently a thread about MTTK coupling on the list with the conclusion that
> MTTK is so far not stable, but please check the archives to assure this.
>
> /Flo
>
>> > On Tue, Nov 20, 2012 at 10:10 PM, Justin Lemkul  wrote:
>> >>
>> >>
>> >> On 11/20/12 11:26 AM, tarak karmakar wrote:
>> >>>
>> >>> Dear All,
>> >>>
>> >>> I want to keep the pressure at 1.0 bar during the NPT simulation.
>> >>> But it is fluctuating around 130 bar. So can anyone please inform me
>> >>> whether I have missed any keyword in my .mdp file OR is it because
>> >>> of the tau_p which I set 1s 1.0 ps.
>> >>
>> >>
>> >> Equilibrate with a weak coupling method (Berendsen) and then proceed
>> >> using better algorithms.
>> >>
>> >> -Justin
>> >>
>> >>
>> >>> Thanks
>> >>>
>> >>> The .mdp file is given below
>> >>>
>> >>>
>> >>>
>> >>> ; 7.3.3 Run Control
>> >>> integrator  = md-vv; md integrator
>> >>> tinit   = 0 ; [ps] starting time
> for
>> >>> run
>> >>> dt  = 0.001 ; [ps] time step for
>> >>> integration
>> >>> nsteps  = 1500; maximum number of
>> >>> steps to integrate, 0.001 * 15,00,000 = 15 ns
>> >>> nstcomm = 1 ; [steps] frequency of
>> >>> mass motion removal
>> >>> comm_grps   = Protein Non-Protein   ; group(s) for center
>> >>> of mass motion removal
>> >>>
>> >>> ; 7.3.8 Output Control
>> >>> nstxout = 1; [steps] freq to write
>> >>> coordinates to trajectory
>> >>> nstvout = 1; [steps] freq to write
>> >>> velocities to trajectory
>> >>> nstfout = 1; [steps] freq to write forces
>> >>> to trajectory
>> >>> nstlog  = 1000   ; [steps] freq to write
>> >>> energies to log file
>> >>> nstenergy   = 1000   ; [steps] freq to write
>> >>> energies to energy file
>> >>> nstxtcout   = 1000   ; [steps] freq to write
>> >>> coordinates to xtc trajectory
>> >>> xtc_precision   = 1000  ; [real] precision to write
>> >>> xtc trajectory
>> >>> xtc_grps= System; group(s) to write to xtc
>> >>> trajectory
>> >>> energygrps  = System; group(s) to write to energy
> file
>> >>>
>> >>> ; 7.3.9 Neighbor Searching
>> >>> nstlist = 1 ; [steps] freq to update
> neighbor
>> >>> list
>> >>> ns_type = grid  ; method of updating neighbor
> list
>> >>> pbc = xyz   ; periodic boundary conditions
>> >>> in all directions
>> >>> rlist   = 1.2   ; [nm] cut-off distance for
>> >>> the short-range neighbor list
>> >>>
>> >>> nsttcouple  = 1
>> >>> nstpcouple  = 1
>> >>>
>> >>> ; 7.3.10 Electrostatics
>> >>> coulombtype = PME 

Re: [gmx-users] Re,i don't know how can i determine emtol

[Ivan Gladich]

On 11/21/2012 11:41 AM, Ali Alizadeh wrote:

Dear Ivan

Thank you for your reply,

Dear Ali
please keep the discussion open to everybody...
In this way you will be sure that someone else  will read and interact 
with us, correcting me if I say something wrong to you..;-)

1- In your opinion, Can i simulate that system?

In my (humble) opinion:

1)Of course you can simulate that system...however  I doubt that, 
without starting from the exact initial configuration with the exactly 
same set-up, you can get the same results (i.e. see the nucleation).
The onset of ice nucleation is a random process and requires very long 
simulation (the paper that you posted was analysing micro-second 
trajectories!!).
There is the risk that you could try several different initial 
configurations at several temperature without getting anything.

 However, read carefully that paper, I do not remember all the details.

If you are interested in ice crystal growth, I would suggest to start 
with an initial water/ice system: at temperature below the melting one 
you will see formation of new ice starting from the initial ice matrix.

There are several works in literature on this.

2- How can i use rigid TIP4P model of water?
2)  I would rather use other water model that have been explicitly 
tested  for Ice


(e.g. TIP4P/2005, TIP4P/Ice, TIP5P-Ew, NE6)

Best
Ivan

Sincerely

Ali Alizadeh




On 11/21/2012 09:43 AM, Ivan Gladich wrote:

Dear Ali
the paper that you are citing is using a rigid TIP4P water model
As far as I know, emtol is relevant only for minimization or molecular 
dynamics with shell particle or flexible constraints.

Therefore, as Justin told you, the emtol value should be irrelevant.

Concerning this paper, I would like to warn you that h_omogeneous ice 
nucleation from bulk water_ with explicit water molecule is very rare 
event...
It's depends from the initial condition and it requires very long 
simulations.
Indeed, if I remember well this paper, they observed homogeneous ice 
crystal formation in only one of their trajectories...read carefully 
the paper!


Best
Ivan



On 11/21/2012 07:47 AM, Ali Alizadeh wrote:

On 11/20/12 3:38 PM, Ali Alizadeh wrote:
  Dear Justin

Thank you ,

This link is the paper that i want to reproduce its results,

Title: Molecular dynamics simulation of
the ice nucleation and growth
process leading to water freezing

http://www.nature.com/nature/journal/v416/n6879/pdf/416409a.pdf




I am using MD instead of steep, and i have a problem, I do not know
value of emtol so that energy of system reaches to -51 kj/mol, i
determine it then run it but it reaches to -30 kj/mol(only for 1ns)

original results :

   http://alichemical.persiangig.com/document/11.jpg


Justin wrote:

>  The value of emtol is only relevant in EM and has no
relationship whatsoever to
>  MD.  In fact, this keyword is ignored if an EM algorithm
is not chosen as the
>integrator.

This means  When i use the md-vv integrator, emtol is ignored.

>No one can help you if you don't fully describe what
you're doing.  That appears
>to be a figure from some paper - what's going on?  If it
is from a paper, what
>were the methods?  How was the plot produced?  Otherwise
no one will have any
idea what's going on.  You can't just force a system to
adopt some series of
>configurations that yield a given potential energy.

>Please describe in full what you are doing, and provide
answers to all the
>questions posed above, or else I'm afraid I'm not going to
have anything else
>useful to say.

 -Justin








--
--
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic

Tel: +420775504164
e-mail: ivan.glad...@uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
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Re: [gmx-users] how to repeat simulation correctly?

[Felipe Pineda, PhD]

So how would you repeat the (let be it converged) simulation from 
different starting conditions in order to add that valuable statistics 
you mention?


I think this was Albert's question

Felipe

On 11/21/2012 12:41 PM, Mark Abraham wrote:

If a simulation ensemble doesn't converge reliably over a given time scale,
then it's not converged over that time scale. Repeating it from different
starting conditions still adds valuable statistics, but can't be a
replicate. Independent replicated observations of the same phenomenon allow
you to assess how likely it is that your set of observations reflect the
underlying phenomenon. The problem in sampling-dependent MD is usually in
making an observation (equating a converged simulation with an observation).

Mark

On Wed, Nov 21, 2012 at 8:12 AM, Albert  wrote:


hello:

   I am quite confused on how to repeat our MD in Gromacs. If we started
from the same equilibrated .gro file with "gen_vel= no" in md.mdp,
we may get "exactly" the same results which cannot be treated as reasonable
repeated running. However, if we use "gen_vel=yes" for each round of
running, sometimes our simulation may not converged at our simulated time
scale and we may get two results with large differences.

   So I am just wondering how to perform repeated MD in Gromacs in a
correct way so that our results can be acceptably repeated?

thank you very much.
Albert
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--
+---+
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| Computational Chemist - Postdoc   |
| Computational Chemistry and   |
| Biochemistry Laboratory   |
| School of Natural Sciences|
| Linnaeus University   |
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Re: [gmx-users] how to repeat simulation correctly?

[Mark Abraham]

If a simulation ensemble doesn't converge reliably over a given time scale,
then it's not converged over that time scale. Repeating it from different
starting conditions still adds valuable statistics, but can't be a
replicate. Independent replicated observations of the same phenomenon allow
you to assess how likely it is that your set of observations reflect the
underlying phenomenon. The problem in sampling-dependent MD is usually in
making an observation (equating a converged simulation with an observation).

Mark

On Wed, Nov 21, 2012 at 8:12 AM, Albert  wrote:

> hello:
>
>   I am quite confused on how to repeat our MD in Gromacs. If we started
> from the same equilibrated .gro file with "gen_vel= no" in md.mdp,
> we may get "exactly" the same results which cannot be treated as reasonable
> repeated running. However, if we use "gen_vel=yes" for each round of
> running, sometimes our simulation may not converged at our simulated time
> scale and we may get two results with large differences.
>
>   So I am just wondering how to perform repeated MD in Gromacs in a
> correct way so that our results can be acceptably repeated?
>
> thank you very much.
> Albert
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Re,i don't know how can i determine emtol

[Ivan Gladich]

Dear Ali
the paper that you are citing is using a rigid TIP4P water model
As far as I know, emtol is relevant only for minimization or molecular 
dynamics with shell particle or flexible constraints.

Therefore, as Justin told you, the emtol value should be irrelevant.

Concerning this paper, I would like to warn you that h_omogeneous ice 
nucleation from bulk water_ with explicit water molecule is very rare 
event...
It's depends from the initial condition and it requires very long 
simulations.
Indeed, if I remember well this paper, they observed homogeneous ice 
crystal formation in only one of their trajectories...read carefully the 
paper!


Best
Ivan



On 11/21/2012 07:47 AM, Ali Alizadeh wrote:

On 11/20/12 3:38 PM, Ali Alizadeh wrote:
  Dear Justin

Thank you ,

This link is the paper that i want to reproduce its results,

Title: Molecular dynamics simulation of
the ice nucleation and growth
process leading to water freezing

http://www.nature.com/nature/journal/v416/n6879/pdf/416409a.pdf




I am using MD instead of steep, and i have a problem, I do not know
value of emtol so that energy of system reaches to -51 kj/mol, i
determine it then run it but it reaches to -30 kj/mol(only for 1ns)

original results :

   http://alichemical.persiangig.com/document/11.jpg


Justin wrote:

   >  The value of emtol is only relevant in EM and has no
relationship whatsoever to
   >  MD.  In fact, this keyword is ignored if an EM algorithm
is not chosen as the
>integrator.

This means  When i use the md-vv integrator, emtol is ignored.

>No one can help you if you don't fully describe what
you're doing.  That appears
>to be a figure from some paper - what's going on?  If it
is from a paper, what
>were the methods?  How was the plot produced?  Otherwise
no one will have any
idea what's going on.  You can't just force a system to
adopt some series of
   >configurations that yield a given potential energy.

  >Please describe in full what you are doing, and provide
answers to all the
>questions posed above, or else I'm afraid I'm not going to
have anything else
  >useful to say.

 -Justin





--
--
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic

Tel: +420775504164
e-mail: ivan.glad...@uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
-

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