[gmx-users] How to calculate chemical shift?

[Xianwei Wang]

 Dear gmx users:
 I would like to calculate chemical shift using g_chi ,but the result has 
only :
 *** Chemical shifts from the chemical shift index ***

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. S. Wishart and A. M. Nip
Protein Chemical Shift Analysis: A Practical Guide
Biochem. Cell Biol. 76 (1998) pp. 153-163
  --- Thank You ---  

 Residuedelta Cadelta Hadelta COdelta Cb
HIS2   -0.6992350.129631   -0.9645560.626928

Residue HIS2
 Angle [   AI,   AJ,   AK,   AL]  #tr/ns  S^2D 

   Phi [8,7,9,   22]   48.150.77
   Psi [7,9,   22,   23]   37.800.13
what I want is chemical shift of atom N. How could I get it ?
Best wishes!
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Re: [gmx-users] analysing of the long trajectories

[Chandan Choudhury]

trjconv -dt

use dt flag with the utility trjconv

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Fri, Jun 15, 2012 at 12:07 PM, a a  wrote:

>  try ptraj
>
> --
> Date: Fri, 15 Jun 2012 10:18:40 +0400
> Subject: Re: [gmx-users] analysing of the long trajectories
> From: jmsstarli...@gmail.com
> To: gmx-users@gromacs.org
>
>
> By the way,
>
> I'm also looking for a most trivial way for extraction of pdb files from
> my trajectory on the desired intervals. E.g I have trajectory consisted of
> 5000 frames and I want to obtain 10 pdb files every each 500 frames ( or
> selected time interval as the alternative ).
>
> Commonly I do it manually via VMD ( save pdb option) but is there any
> automatic way to do it expecially for a long trajectories?
>
>
> James
>
> -- gmx-users mailing list gmx-users@gromacs.org
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Re: [gmx-users] Insertion protein in the membrane via G_membed

[James Starlight]

I've found main reason of such crushes. It was due to the individual
internal waters wich I've included to my model as the buried to the protein
interiour ( the coordinates were copppied form X-ray structure of the same
protein).

By the way I have already performed  the same simulation with the
inclussion of the same X-ray waters but in different system with
membrane-mimicking env. consisted of Ccl4 in water. As the result there
have not been any problems with that system.

Finally I have some question about G_membed acceleration.  I've noticed
that the process of insertion of the protein in the membrane is very long
(actually it's only 50ps simulation).

During procesing of my system I've obtained notes like

NOTE 4 [file topol.top, line 19511]:
  For energy conservation with LINCS, lincs_iter should be 2 or larger.

NOTE 1 [file gmembed.mdp]:
  You are using a cut-off for VdW interactions with NVE, for good energy
  conservation use vdwtype = Shift (possibly with DispCorr)

NOTE 2 [file gmembed.mdp]:
  You are using a cut-off for electrostatics with NVE, for good energy
  conservation use coulombtype = PME-Switch or Reaction-Field-zero

The parameters for long-range and short-range interactions I've used from
my typical simulation on the lipid Gromos56-ff ( presented in the Justin's
tutorial).

Is there any other  parameters for that object wich are most suitable for
G_membed ?

James


2012/6/14 James Starlight 

> Mark,
>
> I've used commands provided in the G_membed manual
>
>g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000
>
> or
>
>g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000
> -zinit 1.1 -zend 1.0 -nz 100
>
>
> In both cases I've obtained the same message
>
> There are 122 lipids in the membrane part that overlaps the protein.
> The area per lipid is 0.5002 nm^2.
> Maximum number of lipids that will be removed is 45.
>
> and eventually only 10 lipids were removed. Also I've tried to do this on
> another pope bilayer (consisted of bigger lipids with properly equilirated
> ) but I've obtained exactly the same results.
>
>
> James
>
> 2012/6/14 Mark Abraham 
>
>>  On 14/06/2012 4:39 PM, James Starlight wrote:
>>
>> Dear Gromacs Users!
>>
>> I've forced with the problem durin insertion of my protein into
>> pre-equilibrated bilayer via G_Membed.
>>
>> I've done all steps in accordance to the KALP tutorial ( I've oriented
>> both membrane as well as the protein in the same dimensions merged both
>> topologies and gro files in the merged.gro file ) but after processed via
>> grompp I've recieved warning
>>
>> WARNING 1 [file gmembed.mdp]:
>>   Can not exclude the lattice Coulomb energy between energy groups
>>
>>
>> You've asked about this before...
>> http://lists.gromacs.org/pipermail/gmx-users/2011-November/066002.html
>>
>>
>> if I scip this message by maxwarn oprtins, g_membed remove only 10 lipids
>> ( while > 40 are overlapped with the protein ) and during further
>> g_membed's md_run I've obtained lincs warning and my system is crushed .
>>
>>
>> Have you followed g_membed -h and their published method? You've not
>> shown your command lines, so it's impossible for anyone to know what you're
>> doing.
>>
>> Mark
>>
>>
>>
>>
>> I'm using berger lipids and that mdp file for the G_membed
>>
>> integrator = md
>> energygrps  = Protein
>> freezegrps = Protein
>> freezedim  = Y Y Y
>> energygrp_table
>> energygrp_excl = Protein Protein
>>
>>
>>
>> emtol= 1000.0  ; Stop minimization when the maximum force <
>> 1000.0 kJ/mol/nm
>> emstep  = 0.01  ; Energy step size
>> nsteps= 5  ; Maximum number of (minimization) steps
>> to perform
>>
>> ; Bond parameters
>> constraint_algorithm = lincs; holonomic constraints
>> constraints= all-bonds; all bonds (even heavy atom-H
>> bonds) constrained
>> lincs_iter= 1; accuracy of LINCS
>> lincs_order= 4; also related to accuracy
>> ; Neighborsearching
>> ns_type= grid; search neighboring grid cels
>> nstlist= 5; 10 fs
>> rlist= 1.2; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.2; short-range electrostatic cutoff (in nm)
>> rvdw= 1.2; short-range van der Waals cutoff (in nm)
>> ; Electrostatics
>> coulombtype= PME; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order= 4; cubic interpolation
>> fourierspacing= 0.16; grid spacing for FFT
>> pbc= xyz; 3-D PBC
>>
>>
>> Could you tell me where is the problem in my case might be?
>>
>>
>> James
>>
>>
>>
>>
>> --
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RE: [gmx-users] analysing of the long trajectories

[a a]

try ptraj

Date: Fri, 15 Jun 2012 10:18:40 +0400
Subject: Re: [gmx-users] analysing of the long trajectories
From: jmsstarli...@gmail.com
To: gmx-users@gromacs.org

By the way,

I'm also looking for a most trivial way for extraction of pdb files from my 
trajectory on the desired intervals. E.g I have trajectory consisted of 5000 
frames and I want to obtain 10 pdb files every each 500 frames ( or selected 
time interval as the alternative ).


Commonly I do it manually via VMD ( save pdb option) but is there any automatic 
way to do it expecially for a long trajectories?


James


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[gmx-users] current directory files

[tarak karmakar]

Dear All,


  In my protein pdb file I have changed some of the amino acid residue
names. So accordingly I have changed corresponding residue names in force
filed files and kept all the files [ modified and unmodified ] in my
current working directory. Those files are

1) atomtypes.atp
2) aminoacids.rtp
3) ffnonbonded.itp
4) ffbonded.itp
5) spc.itp
6) ions.itp

now while giving the command
pdb2gmx -f prot.pdb -o prot.gro -p toplogy.top

how can I make use of all these force field files present in my current
working directory ?
Thanks in advance.



-- 
*Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809 *
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Re: [gmx-users] analysing of the long trajectories

[James Starlight]

By the way,

I'm also looking for a most trivial way for extraction of pdb files from my
trajectory on the desired intervals. E.g I have trajectory consisted of
5000 frames and I want to obtain 10 pdb files every each 500 frames ( or
selected time interval as the alternative ).

Commonly I do it manually via VMD ( save pdb option) but is there any
automatic way to do it expecially for a long trajectories?


James
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[gmx-users] simulating dimer proteins

[delara aghaie]

Dear Gromacs users
I want to compare some properties of two Interferons via MD simulation.
One comes with pdb ID : 1ITF. (It has 24 Models in single pdb file, but each 
model with single chain.) I did pdb2gmx on this.

The other is with pdb ID of : (1RFB). This has two chanis

DBREF  1RFB A    1   119  UNP    P07353   IFNG_BOVIN  24    142
DBREF  1RFB B    1   119  UNP    P07353   IFNG_BOVIN  24    142
---

Now the question: Is it wise to select only chain A and do the simulations on 
it in order to compare with the 1ITF, which has one chain?.
I have read about simulating multiple chains in manual. But I think the 
comparison between a protein with single chain and the other with two chains 
may not be correct. (I want to compare gyration radiuses and secondary 
structures)
 I want to know if it is common to do MD on selected chain of a dimer?

Your help would be greatly appreciated

Regards
D.M
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Re: [gmx-users] analysing of the long trajectories

[James Starlight]

Hi Tsjerk !

I my case I want to compare large-scale dynamics with more local events
like fluctuation of the individual side chains so I suppose that I need
larger number of frames. But how exactly I could define this number for my
100ns trajectory? Commoly I've used 5000 value for all nst* options in MDP
file but that produce trajectories with ~ 10.000 frames for 100ns. If I
increase this values  from 5000 to 1 could I see dynamics on the level
of the individual side-chains ? ( e.g occurence of salt-bridges or rotamer
isomerisation of the polar side chains during my 100ns trajectory ).


James

2012/6/12 Tsjerk Wassenaar 

> Hi James,
>
> Large-scale protein dynamics is low-frequency motion, so you don't
> need a high time resolution. For large-scale dynamics alone, something
> in the range of 1000-2500 frames should be sufficient, depending on
> the size of the system. Note that larger systems require more frames,
> as there will be more large scale dynamics to characterize.
>
> Cheers,
>
> Tsjerk
>
>
>
> On Tue, Jun 12, 2012 at 9:29 AM, James Starlight 
> wrote:
> > Mark,
> >
> > Thanks for advise.
> >
> > As I've found in that link the main way to reduce dimension of the output
> > data is the ussage of appropriate nst* params in the mdp file, exclusion
> of
> > the solvent from output and finally ussing compres trajectories.
> >
> > Could you tell me what are the most suitable size for the nst* params for
> > the typical similation in water ( 50-250 ns) where I want to observe both
> > large-scale protein dynamics as well locale flexibility of the individual
> > side chain and solvent molecules ? Typically I've used 5000 for evert
> nst*
> > params but that produce relatively big trajetories even in the xtc format
> >
> > James
> >
> >
> > 2012/6/12 Mark Abraham 
> >>
> >> On 12/06/2012 4:20 PM, James Starlight wrote:
> >>>
> >>> Dear Gromacs Users!
> >>>
> >>>
> >>> I've forced with the problem during analysing of long trajectories
> >>> consisted of > 5000 calculated for average system ( ~ 35000 atoms).
> Commonly
> >>> I use VMD for analysing of such task but in case of long trajectories
> >>> loading this software has been crashed with the memory eror message.
> Could
> >>> you advise me the possible way to solve this problem
> >>
> >>
> >> See
> >>
> http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
> >>
> >>
> >>> or another software for visualisation as well as extraction of the
> >>> selected steps from trajectory as the pdb files ?
> >>
> >>
> >> trjconv -h for command line cut'n'paste.
> >>
> >> Insisting on doing analysis of data .pdb format costs you time and
> space.
> >> If you're having problems with either, then you should revisit whether
> you
> >> need that format.
> >>
> >> Mark
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
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> >> Please search the archive at
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> >
> >
> >
> > --
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>
>
>
> --
> 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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Re: [gmx-users] FEP

[Sai Kumar Ramadugu]

Hi Fabian,
I am trying something similar with Glutamate to Alanine mutation.
Does your dummy atoms i.e., DUM1 have a value of 0.0 for sigma and epsilon
during all three steps or only in step 2?

Thanks for the time,

Sai

On Thu, Apr 26, 2012 at 10:43 AM, Fabian Casteblanco <
fabian.castebla...@gmail.com> wrote:

> Hello all,
>
> This is in reply to Michael shirts a while ago on a FEP of a R-CH3 to
> an R-H group.  Below is the orignal email.  I recently tested out
> mutating a CH3-CH3-(3dummy atoms) molecule on both sides in order to
> test out that a peturbation would give you a total of 0.  forcefield
> used was CGenFF
>
> So for procedure was that I turned the CH3 group on the left to an H
> with 3 dummy atoms and I turned an H and 3 dummy atoms on the right to
> a CH3 group, essentially mutating the molecule to another version of
> itself (should give you a total dG of 0 if it works).
>
> STEP 1. (uncharging everything except the -CH2 group inbetween both
> sides     CH3-CH2-HD3)  *D are dummy atoms
>  [ atoms ]
> ;  nr  type  resnr  residatom  cgnr  chargemasstotal_charge
>1CG331 1   SIM   C1 1-0.27
>12.0110 CG331   0.00 12.0110
>2 HGA3 1   SIM  H11 2 0.09
>1.00800 HGA30.00 1.00800
>3 HGA3 1   SIM  H12 3 0.09
>1.00800 HGA30.00 1.00800
>4 HGA3 1   SIM  H13 4 0.09
>1.00800 HGA30.00 1.00800
>5CG331 1   SIM   C2 5-0.27  12.0110
> CG331
> -0.1812.0110
>6 HGA3   1   SIM  H21 6   0.09
>7 HGA3   1   SIM  H22 7   0.09
>8 HGA3   1   SIM  H23 8   0.09  1.00800
> HGA30.00 1.00800
>9  DUM   1   SIM  H31 9   0.00  1.00800
>   10  DUM   1   SIM  H3210   0.00  1.00800
>   11  DUM   1   SIM  H3311   0.00  1.00800
>
> STEP 2.  (mutation of groups.   CH3-CH2-HD3 becomes D3H-CH2-CH3)
> [ atoms ]
> ;  nr  type  resnr  residatom  cgnr  chargemasstotal_charge
>1CG331  1   SIM   C1  1   0.00
>12.0110 HGA30.00   1.00800
>2 HGA3  1   SIM  H11  2   0.00
>1.00800 DUM 0.00   1.00800
>3 HGA3  1   SIM  H12  3   0.00
>1.00800 DUM 0.00   1.00800
>4 HGA3  1   SIM  H13  4   0.00  1.00800
> DUM
>   0.001.00800
>5CG331  1   SIM   C2  5  -0.18
>6 HGA31   SIM  H21 6  0.09
>7 HGA31   SIM  H22 7  0.09
>8 HGA31   SIM  H23 8  0.00
>1.00800 CG331   0.00   12.0110
>9  DUM1   SIM  H31 9  0.00
>  1.00800 HGA30.00
>  1.00800
>   10  DUM1   SIM  H3210  0.00  1.00800
> HGA30.00
>  1.00800
>   11  DUM1   SIM  H3311  0.00
>1.00800 HGA30.00   1.00800
>
> STEP3.  (opposite of step1)
> [ atoms ]
> ;  nr  type  resnr  residatom  cgnr  chargemasstotal_charge
>1 HGA3   1   SIM C1 1 0.00  12.0110
> HGA3
>  0.091.00800
>2  DUM   1   SIMH11 2 0.00
> 1.00800 DUM0.00   1.00800
>3  DUM   1   SIMH12 3 0.00
> 1.00800 DUM0.00   1.00800
>4  DUM   1   SIMH13 4 0.00
> 1.00800 DUM0.00   1.00800
>5CG331   1   SIM C2 5-0.18
>  12.0110 CG331
>  -0.27   12.0110
>6 HGA3   1   SIM  H21 6   0.09
>7 HGA3   1   SIM  H22 7   0.09
>8CG331   1   SIM  H23 8   0.00
> 1.00800 CG331 -0.27   12.0110
>9 HGA3   1   SIM  H31 9   0.00
> 1.00800 HGA30.09  1.00800
>   10 HGA3   1   SIM  H3210   0.00
> 1.00800 HGA30.09  1.00800
>   11 HGA3   1   SIM  H3311   0.00
> 1.00800 HGA30.09  1.00800
>
> So in the end, the procedure worked using the g_bar method.  I took 20
> simulations for steps 1 and 3 and 50 simulations for step 2.  Here are
> the results:
>
> Step1: -37.62 +/- 0
> Step2:  -0.12 +/- 0.24
> Step3:  37.68 +/- 0.13
> TOTAL ~ -0.06 kJ/mol  which is expected
>
> My question is that I did something similar for a larger molecule (65
> atoms) and someone said before that step 1 and 3 should be very small.
>  I'm getting values in the near -20 kJ/mol for step 1 and 3.  I feel
> it should be straightforward since I'm simply uncharging 

[gmx-users] RE: Re: g_lie reproducibility

[Tom Dupree]

Hi Mark,
Thanks for the catch on the transcription error, I think I have found it 
::embarrassed::.
The repeated final value is still perplexing me. I have checked both my .xvg 
from g_energy and the .edr file with gmxdump. In both cases the final step 
(time value) only occurs once, and the second last time point has different 
values. This is a single run so I don't think I should have concatenation 
issues?

I just checked the counts and there are 476 time points in the energy file and 
477 in the g_lie file.

All the best,
Tom

On 14/06/2012 3:56 PM, Tom Dupree wrote:
> Greetings all,
> I can't manually reproduce g_lie results.
> After raging at excel for a while I think I have found a bug.
>
> Here is my first time point,
> Reported by g_lie to be 35.0073
> > From energy file
> Lj_complex =-130.762
> Coul_complex = -286.746
> My constants specified to g_lie
> Clj = Alpha = lj_const = 0.181
> Cqq = Beta = coul_const = 0.43
> Elj = Lj_solv = -166
> Eqq = Coul_solv = -263
>
> Therefore
> Lj_diff = 35.238
> Coul_diff = -23.746
>
> Hence
> Lj_diff x lj_const = 6.378
> Coul_diff x coul_const = -10.211
>
> And there is no way I can add those to get 35.0073
>
> However I can get this value using the following
> Coul_complex - lj_solv = -120.746
> Lj_complex - coul_solv = 132.2378
> -120.746 x lj_const = -120.746 x 0.181 = -21.855
> 132.2378 x coul_const = 56.86225
> Sum = 35.00726
>
> In short I think the g_lie calculation has swapped its variables, Elj instead 
> of Eqq and vice versa.

I think it's rather more likely you've made a transcription error going 
to Excel. You can check the code of src/tools/gmx_lie.c for exactly this 
kind of purpose, but I can't see any problem with it.

>
> One other thing I have noticed is that when calculating the average g_lie 
> uses the final value twice, is there a reason for this?
>
> e.g.
>
>   994 24.9397
>   996 43.3382
>   998 40.5714
> 1000 40.5585
> 1000 40.5585
>

Inspect your energy file with gmxdump - I think you've managed to 
duplicate the final frame at an earlier point of your workflow. eneconv 
has options to prevent such duplicates occuring during concatenation, 
etc. In any case, g_lie just eats what you give it...

Mark


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[gmx-users] Bootstrapping using g_wham

[rainy908]

Hi,

I am currently using bootstrapping in g_wham to estimate the uncertainty in my 
PMF.  I use a number of 1000 bootstraps.  

/software/gromacs/gromacs-4.0.7-plumed-1.2.0-x86_64/bin//g_wham \
 -ip gwham.dat \
 -bins 5000 \
 -hist histo.xvg \
 -bsres bsResult.xvg \
 -nBootstrap 1000

This process has been running on 1 node for the past 4 days straight, and I am 
not sure when it will ever finish.  Should I be concerned?

Thanks again,
Lili


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[gmx-users] Force constant in g_wham

[rainy908]

Dear gmx-users,

I am writing to clarify that the force constant kappa for g_wham corresponds to 
K_i itself, and not the quantity (1/2)*K_i in the umbrella potential W_i(ξ) = 
(K_i/2)*(ξ-ξ_i)^2.

I recall reading somewhere that the force constant sometimes includes the (1/2) 
term in front of K_i, and sometimes not.

Thank you,
Lili

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[gmx-users] Diameter of the micelle

[Christopher Neale]

You first need to obtain an .xtc in which the micelle is entirely within the 
unit cell in every frame:

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

You can then use g_gyrate to get the radius of gyration or g_rdf to get the 
radial

distribution function from the micelle COM or some other tool compute the 
diameter (but note

that there are many ways to define the "diameter" of an object with a rough 
surface).

Chris.

-- original message --

I am working with an emulsion water/n-dodecane in a box of 29nm.

I wish  to know  how I can to get the diameter of the micelle in the frame,

then I need to measuring the average diameter of the micelle in each frame.

Thanks for your help!!
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[gmx-users] Diameter of the micelle

[Angie Paola Macias Lozano]

Hi,
I am working with an emulsion water/n-dodecane in a box of 29nm. I wish  to 
know  how I can to get the diameter of the micelle in the frame, then I need to 
measuring the average diameter of the micelle in each frame.

Thanks for your help!!
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Re: [gmx-users] dodssp segmentation fault SOLVED for DEBIAN

[raf ponsaerts]

Indeed, I am still using Gromacs-4.5.5, downloaded from gromacs.org on
Debian GNU/Linux 6.0.5 (48-core AMD64) with kernel 3.1.1 and patched
do_dssp manually as has been done for the newer releases. Works fine
with the new dssp-2.0.4 release.


raf

On Thu, 2012-06-14 at 13:39 +0200, Erik Marklund wrote:
> This issue has been resolved so the next official release of gromacs
> will be capacle of using the newer versions of dssp.
> 
> 
> Erik
> 
> 14 jun 2012 kl. 12.57 skrev Denis Kazakiewicz:
> 
> > Wow, just did that.
> > In Debian have to use 4.5.5-2 version of Gromacs from sid
> > repository.
> > Still have to use the oldest dssp
> > http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi
> > 
> > It was simply Gromacs issue with no ways around.
> > And it woks:)
> > 
> > Just wondering,
> > What are other efficient ways of analyzing secondary structure
> > instead of dssp? (novice question)
> > Good luck to everybody
> > 
> > 
> > On 14.06.2012 11:59, Denis Kazakiewicz wrote:
> > > Hello
> > > Dear Gromacs users.
> > > This is many times discussed issue, however nothing seems to work
> > > so far
> > > 
> > > do_dssp returns "Segmentation fault"
> > > 
> > > It is the oldest version of dssp: dsspcmbi
> > > Gromacs 4.5.5 on Debian i386
> > > I did use export DSSP=/path to dssp
> > > 
> > > 1. What is possibly could be?
> > > 2. Any other efficient ways of analyzing secondary structure
> > > without do_dssp (with VMD, may be)?
> > > 
> > > THANKS in advance
> > 
> > -- 
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
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> > 
> 
> ---
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 6688fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
> 
> 


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Re: [gmx-users] dodssp segmentation fault SOLVED for DEBIAN

[Erik Marklund]

This issue has been resolved so the next official release of gromacs will be 
capacle of using the newer versions of dssp.

Erik

14 jun 2012 kl. 12.57 skrev Denis Kazakiewicz:

> Wow, just did that.
> In Debian have to use 4.5.5-2 version of Gromacs from sid repository.
> Still have to use the oldest dssp
> http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi
> 
> It was simply Gromacs issue with no ways around.
> And it woks:)
> 
> Just wondering,
> What are other efficient ways of analyzing secondary structure instead of 
> dssp? (novice question)
> Good luck to everybody
> 
> 
> On 14.06.2012 11:59, Denis Kazakiewicz wrote:
>> Hello
>> Dear Gromacs users.
>> This is many times discussed issue, however nothing seems to work so far
>> 
>> do_dssp returns "Segmentation fault"
>> 
>> It is the oldest version of dssp: dsspcmbi
>> Gromacs 4.5.5 on Debian i386
>> I did use export DSSP=/path to dssp
>> 
>> 1. What is possibly could be?
>> 2. Any other efficient ways of analyzing secondary structure without do_dssp 
>> (with VMD, may be)?
>> 
>> THANKS in advance
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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Re: [gmx-users] dodssp segmentation fault SOLVED for DEBIAN

[Denis Kazakiewicz]

Wow, just did that.
In Debian have to use 4.5.5-2 version of Gromacs from sid repository.
Still have to use the oldest dssp
http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi

It was simply Gromacs issue with no ways around.
 And it woks:)

Just wondering,
 What are other efficient ways of analyzing secondary structure instead 
of dssp? (novice question)

Good luck to everybody


On 14.06.2012 11:59, Denis Kazakiewicz wrote:

Hello
Dear Gromacs users.
This is many times discussed issue, however nothing seems to work so far

do_dssp returns "Segmentation fault"

It is the oldest version of dssp: dsspcmbi
Gromacs 4.5.5 on Debian i386
I did use export DSSP=/path to dssp

1. What is possibly could be?
2. Any other efficient ways of analyzing secondary structure without 
do_dssp (with VMD, may be)?


THANKS in advance


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[gmx-users] dodssp segmentation fault

[Denis Kazakiewicz]

Hello
Dear Gromacs users.
This is many times discussed issue, however nothing seems to work so far

do_dssp returns "Segmentation fault"

It is the oldest version of dssp: dsspcmbi
Gromacs 4.5.5 on Debian i386
I did use export DSSP=/path to dssp

1. What is possibly could be?
2. Any other efficient ways of analyzing secondary structure without 
do_dssp (with VMD, may be)?


THANKS in advance
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[gmx-users] Re: Effect of vdwradii.dat

[anna.duncan]

Thanks, Mark.  I tried this and there is, indeed, no difference.

Anna

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Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

[Justin A. Lemkul]

On 6/14/12 4:06 AM, ms wrote:

Ok, I tried some of your suggestions and the Coulomb-SR energies still fall down
very quickly.

I wonder if:

On 13/06/12 16:59, Justin A. Lemkul wrote:

4. What happens when you use the Andersen thermostat? That's not
implemented yet for CPU calculations (though it was recently pushed into
the 4.6 development branch). Your comment regarding GPU is fine, but I
would think grompp would complain.


maybe mdrun *tries* to use Andersen but since it's not fully implemented for
CPUs it makes odd artefacts?



The .log file should tell you for sure.  You can also try a different algorithm 
and see if you observe the same behavior.


-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] Protein near the edges of simulation box

[Tsjerk Wassenaar]

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Cheers,

Tsjerk

On Thu, Jun 14, 2012 at 10:26 AM, Shima Arasteh
 wrote:
>
> Dear gmx friends,
>
> I put a protein in a simulation box filled of water molecules and entered
> the mdrun command. After the simulation, I found the protein near one of the
> edges of the box and not in center. What is the problem? Anyone may suggest
> me?
> Does it mean that the simulation is meaningless?
> I expect the protein to stay in the center of box and goes unfold by passing
> the time.
>
> Thanks in advance
> Sincerely,
> Shima
>
>
>
> --
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-- 
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] Protein near the edges of simulation box

[Shima Arasteh]

Dear gmx friends,

I put a protein in a simulation box filled of water molecules and entered the 
mdrun command. After the simulation, I found the protein near one of the edges 
of the box and not in center. What is the problem? Anyone may suggest me? 

Does it mean that the simulation is meaningless? 

I expect the protein to stay in the center of box and goes unfold by passing 
the time.

 
Thanks in advance

Sincerely,
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Re: [gmx-users] (3x3) Hessian matrix without minimization

[Mark Abraham]

On 14/06/2012 6:10 PM, Hyuntae Na wrote:

> Message: 1
> Date: Thu, 14 Jun 2012 17:19:51 +1000
> From: Mark Abraham 
> Subject: Re: [gmx-users] (3x3) Hessian matrix without minimization
> To: Discussion list for GROMACS users 
> Message-ID: <4fd99097.90...@anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 14/06/2012 5:04 PM, Hyuntae Na wrote:
> > Dear All,
> >
> > I want to get a hessian matrix without minimizing a protein molecule.
> > Essentially, I want to get the 3x3 hessian matrice of each atom 
(which
> > is the diagonal term of the 3n x 3n hessian matrix). Would you 
help me

> > to get it?
>
> Check out manual section 7.4 for hints on which tools are useful for 
you

> - then appendix D for more details.
>

I had done the NMA (Normal Mode Analysis) with sequentially calling 
pdb2gmx, grompp, mdrun, grompp_d, mdrun_d, and gmxdump_d in order to 
minimize the protein structure with L-BFGS (with the final 
minimization step with mdrun_d), and in order to get the hessian 
matrix with text format.


I especially want to get the *hessian matrix with a non-minimized 
protein conformation*.


Doesn't choosing integrator = nm in your .mdp just do that?

Mark
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Re: [gmx-users] (3x3) Hessian matrix without minimization

[Hyuntae Na]

> Message: 1
> Date: Thu, 14 Jun 2012 17:19:51 +1000
> From: Mark Abraham 
> Subject: Re: [gmx-users] (3x3) Hessian matrix without minimization
> To: Discussion list for GROMACS users 
> Message-ID: <4fd99097.90...@anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> On 14/06/2012 5:04 PM, Hyuntae Na wrote:
> > Dear All,
> >
> > I want to get a hessian matrix without minimizing a protein molecule. 
> > Essentially, I want to get the 3x3 hessian matrice of each atom (which 
> > is the diagonal term of the 3n x 3n hessian matrix). Would you help me 
> > to get it?
> 
> Check out manual section 7.4 for hints on which tools are useful for you 
> - then appendix D for more details.
>  I had done the NMA (Normal Mode Analysis) with sequentially calling pdb2gmx, 
> grompp, mdrun, grompp_d, mdrun_d, and gmxdump_d in order to minimize the 
> protein structure with L-BFGS (with the final minimization step with 
> mdrun_d), and in order to get the hessian matrix with text format. I 
> especially want to get the *hessian matrix with a non-minimized protein 
> conformation*. Thanks. Best regards,-- Hyuntae
> Mark
> -- next part ------
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Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

[ms]

Ok, I tried some of your suggestions and the Coulomb-SR energies still 
fall down very quickly.


I wonder if:

On 13/06/12 16:59, Justin A. Lemkul wrote:

4. What happens when you use the Andersen thermostat? That's not
implemented yet for CPU calculations (though it was recently pushed into
the 4.6 development branch). Your comment regarding GPU is fine, but I
would think grompp would complain.


maybe mdrun *tries* to use Andersen but since it's not fully implemented 
for CPUs it makes odd artefacts?



--
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http://devicerandom.org
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Re: [gmx-users] protein near the edges of simulation box

[Mark Abraham]

On 14/06/2012 5:47 PM, Shima Arasteh wrote:

Dear gmx friends,

I put a protein in a simulation box filled of water molecules and 
entered the mdrun command. After the simulation, I found the protein 
near one of the edges of the box and not in center. What is the 
problem? Anyone may suggest me?

Does it mean that the simulation is meaningless?
I expect the protein to stay in the center of box and goes unfold by 
passing the time.


See 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


Mark
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[gmx-users] protein near the edges of simulation box

[Shima Arasteh]

Dear gmx friends,

I put a protein in a simulation box filled of water molecules and entered the 
mdrun command. After the simulation, I found the protein near one of the edges 
of the box and not in center. What is the problem? Anyone may suggest me?

Does it mean that the simulation is meaningless? 

I expect the protein to stay in the center of box and goes unfold by passing 
the time.

 
Thanks in advance

Sincerely,
Shima-- 
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Re: [gmx-users] Insertion protein in the membrane via G_membed

[James Starlight]

Mark,

I've used commands provided in the G_membed manual

   g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000

or

   g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000
-zinit 1.1 -zend 1.0 -nz 100


In both cases I've obtained the same message

There are 122 lipids in the membrane part that overlaps the protein.
The area per lipid is 0.5002 nm^2.
Maximum number of lipids that will be removed is 45.

and eventually only 10 lipids were removed. Also I've tried to do this on
another pope bilayer (consisted of bigger lipids with properly equilirated
) but I've obtained exactly the same results.


James

2012/6/14 Mark Abraham 

>  On 14/06/2012 4:39 PM, James Starlight wrote:
>
> Dear Gromacs Users!
>
> I've forced with the problem durin insertion of my protein into
> pre-equilibrated bilayer via G_Membed.
>
> I've done all steps in accordance to the KALP tutorial ( I've oriented
> both membrane as well as the protein in the same dimensions merged both
> topologies and gro files in the merged.gro file ) but after processed via
> grompp I've recieved warning
>
> WARNING 1 [file gmembed.mdp]:
>   Can not exclude the lattice Coulomb energy between energy groups
>
>
> You've asked about this before...
> http://lists.gromacs.org/pipermail/gmx-users/2011-November/066002.html
>
>
> if I scip this message by maxwarn oprtins, g_membed remove only 10 lipids
> ( while > 40 are overlapped with the protein ) and during further
> g_membed's md_run I've obtained lincs warning and my system is crushed .
>
>
> Have you followed g_membed -h and their published method? You've not shown
> your command lines, so it's impossible for anyone to know what you're doing.
>
> Mark
>
>
>
>
> I'm using berger lipids and that mdp file for the G_membed
>
> integrator = md
> energygrps  = Protein
> freezegrps = Protein
> freezedim  = Y Y Y
> energygrp_table
> energygrp_excl = Protein Protein
>
>
>
> emtol= 1000.0  ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> emstep  = 0.01  ; Energy step size
> nsteps= 5  ; Maximum number of (minimization) steps to
> perform
>
> ; Bond parameters
> constraint_algorithm = lincs; holonomic constraints
> constraints= all-bonds; all bonds (even heavy atom-H
> bonds) constrained
> lincs_iter= 1; accuracy of LINCS
> lincs_order= 4; also related to accuracy
> ; Neighborsearching
> ns_type= grid; search neighboring grid cels
> nstlist= 5; 10 fs
> rlist= 1.2; short-range neighborlist cutoff (in nm)
> rcoulomb= 1.2; short-range electrostatic cutoff (in nm)
> rvdw= 1.2; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype= PME; Particle Mesh Ewald for long-range
> electrostatics
> pme_order= 4; cubic interpolation
> fourierspacing= 0.16; grid spacing for FFT
> pbc= xyz; 3-D PBC
>
>
> Could you tell me where is the problem in my case might be?
>
>
> James
>
>
>
>
> --
> 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] Re: Dihedral Constraints

[bharat gupta]

Sorry for the last reply, I wrote turns with different sequences wrongly,
it's actually the turn with different dihedral constraints. I searched the
gromacs user list , where I found this link , regarding calculation of
dihedral energy of selected residues.  I want to know whether this method
would be useful ??

On Thu, Jun 14, 2012 at 4:16 PM, Mark Abraham wrote:

>  On 14/06/2012 4:57 PM, bharat gupta wrote:
>
> I am not going to compare this with anything , I have to look for
> sequences and their corresponding energies and select the lowest scoring
> ones.
>
>
> You can't compare total energies of different sequences and get a
> meaningful answer. What's the difference in energy between an apple and an
> orange mean? You can compare the average energy of an apple cut into pieces
> with the average energy of a whole apple, but that doesn't necessarily
> relate to the same quantity measured for an orange, either. There's a lot
> of work in measuring a decent *free* energy difference between some states.
>
>
>  I request you to kindly elaborate on freezing some portion of the
> protein. ( I am bit confused as in my case I am fixing the dihedral of turn
> residues which means constraining them simultaneously I want to freeze the
> other region of the protein. )
>
>
> You need to read the link I gave last time and use "constraints" and
> "restraints" in the accepted GROMACS sense in order for people to be able
> to understand your meaning clearly. There are links there to the kind of
> methods that are available. I think you need to do some reading and
> thinking about those :-) If you lock down all the degrees of freedom then
> you can't measure anything relevant.
>
>
> Mark
>
>
>
> On Thu, Jun 14, 2012 at 3:50 PM, Mark Abraham wrote:
>
>>  On 14/06/2012 4:38 PM, bharat gupta wrote:
>>
>> Thanks Sir for the reply... This question is related to my first query
>> that if we constraint the dihedral of the turn residue how can we
>> fix/freeze the movement of other residues.
>>
>>
>>
>> http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
>>
>>
>>  As I am interested in only getting the energy of the hairpin when the
>> turn residues are constrained within a particular phi psi angle range
>>
>>
>>  .. and with what are you going to compare those energies? And what will
>> that comparison mean?
>>
>> Mark
>>
>>
>>
>>
>> On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham 
>> wrote:
>>
>>> On 14/06/2012 12:04 PM, bharat gupta wrote:
>>>
 Thanks for the reply . Is it possible to calculate the dihedral energy
 of certain residues, like in my case for turn residues ??.. How can that be
 done

>>>
>>>  First, seek to define "dihedral energy"... Force fields are not
>>> parametrized such that parts of them are expected to correlate with
>>> observables.
>>>
>>>
>>>
 This another question is regarding energy minimization. Suppose, I
 minimize the the protein solvated in water, the energy value that I get is
 for the whole system or for the protein alone. If it's for the system then
 how can I get the energy for the protein alone.

>>>
>>>  You can define energy groups (see manual) to do this for the nonbonded
>>> contributions. Bonded contributions are easy to do in your case. Whether
>>> this energy is useful for anything is quite another matter.
>>>
>>> Mark
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>>  --
>> 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
>> 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
> http://lists.gromacs.org/mailman/listinf

Re: [gmx-users] Insertion protein in the membrane via G_membed

[Mark Abraham]

On 14/06/2012 4:39 PM, James Starlight wrote:

Dear Gromacs Users!

I've forced with the problem durin insertion of my protein into 
pre-equilibrated bilayer via G_Membed.


I've done all steps in accordance to the KALP tutorial ( I've oriented 
both membrane as well as the protein in the same dimensions merged 
both topologies and gro files in the merged.gro file ) but after 
processed via grompp I've recieved warning


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


You've asked about this before... 
http://lists.gromacs.org/pipermail/gmx-users/2011-November/066002.html


if I scip this message by maxwarn oprtins, g_membed remove only 10 
lipids ( while > 40 are overlapped with the protein ) and during 
further g_membed's md_run I've obtained lincs warning and my system is 
crushed .


Have you followed g_membed -h and their published method? You've not 
shown your command lines, so it's impossible for anyone to know what 
you're doing.


Mark




I'm using berger lipids and that mdp file for the G_membed

integrator = md
energygrps  = Protein
freezegrps = Protein
freezedim  = Y Y Y
energygrp_table
energygrp_excl = Protein Protein



emtol= 1000.0  ; Stop minimization when the maximum force 
< 1000.0 kJ/mol/nm

emstep  = 0.01  ; Energy step size
nsteps= 5  ; Maximum number of (minimization) 
steps to perform


; Bond parameters
constraint_algorithm = lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H 
bonds) constrained

lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cels
nstlist= 5; 10 fs
rlist= 1.2; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2; short-range electrostatic cutoff (in nm)
rvdw= 1.2; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range 
electrostatics

pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
pbc= xyz; 3-D PBC


Could you tell me where is the problem in my case might be?


James




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Re: [gmx-users] (3x3) Hessian matrix without minimization

[Mark Abraham]

On 14/06/2012 5:04 PM, Hyuntae Na wrote:

Dear All,

I want to get a hessian matrix without minimizing a protein molecule. 
Essentially, I want to get the 3x3 hessian matrice of each atom (which 
is the diagonal term of the 3n x 3n hessian matrix). Would you help me 
to get it?


Check out manual section 7.4 for hints on which tools are useful for you 
- then appendix D for more details.


Mark
-- 
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Re: [gmx-users] Re: Dihedral Constraints

[Mark Abraham]

On 14/06/2012 4:57 PM, bharat gupta wrote:
I am not going to compare this with anything , I have to look for 
sequences and their corresponding energies and select the lowest 
scoring ones.


You can't compare total energies of different sequences and get a 
meaningful answer. What's the difference in energy between an apple and 
an orange mean? You can compare the average energy of an apple cut into 
pieces with the average energy of a whole apple, but that doesn't 
necessarily relate to the same quantity measured for an orange, either. 
There's a lot of work in measuring a decent *free* energy difference 
between some states.


I request you to kindly elaborate on freezing some portion of the 
protein. ( I am bit confused as in my case I am fixing the dihedral of 
turn residues which means constraining them simultaneously I want to 
freeze the other region of the protein. )


You need to read the link I gave last time and use "constraints" and 
"restraints" in the accepted GROMACS sense in order for people to be 
able to understand your meaning clearly. There are links there to the 
kind of methods that are available. I think you need to do some reading 
and thinking about those :-) If you lock down all the degrees of freedom 
then you can't measure anything relevant.


Mark




On Thu, Jun 14, 2012 at 3:50 PM, Mark Abraham > wrote:


On 14/06/2012 4:38 PM, bharat gupta wrote:

Thanks Sir for the reply... This question is related to my first
query that if we constraint the dihedral of the turn residue how
can we fix/freeze the movement of other residues.


http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints




As I am interested in only getting the energy of the hairpin when
the turn residues are constrained within a particular phi psi
angle range


.. and with what are you going to compare those energies? And what
will that comparison mean?

Mark





On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:

On 14/06/2012 12:04 PM, bharat gupta wrote:

Thanks for the reply . Is it possible to calculate the
dihedral energy of certain residues, like in my case for
turn residues ??.. How can that be done


First, seek to define "dihedral energy"... Force fields are
not parametrized such that parts of them are expected to
correlate with observables.



This another question is regarding energy minimization.
Suppose, I minimize the the protein solvated in water,
the energy value that I get is for the whole system or
for the protein alone. If it's for the system then how
can I get the energy for the protein alone.


You can define energy groups (see manual) to do this for the
nonbonded contributions. Bonded contributions are easy to do
in your case. Whether this energy is useful for anything is
quite another matter.

Mark

-- 
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http://www.gromacs.org/Support/Mailing_Lists/Search before
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.
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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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--
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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[gmx-users] (3x3) Hessian matrix without minimization

[Hyuntae Na]

Dear All, I want to get a hessian matrix without minimizing a protein molecule. 
Essentially, I want to get the 3x3 hessian matrice of each atom (which is the 
diagonal term of the 3n x 3n hessian matrix). Would you help me to get it? 
Thanks a lot. Best regards,-- Hyuntae-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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