normal ElNeDyn tutorial

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10 years 10 months ago #1598 by martini
ElNeDyn tutorial was created by martini
HI ,

I try to compute the ElNeDyn tutorial but when I try to compile the fortran program noything happen.
I make this command: g77 -O -c pdb2CGpdb-2.1.f
and I obtain this file in output: pdb2CGpdb-2.1.o , I can't do nothing with this file even if I change the permission.
SOmeone obtain this kind of problem???

THanks a lot.

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10 years 10 months ago #1599 by djurre
Replied by djurre on topic ElNeDyn tutorial
The martinize.py scripts creates CG topologies with Elnedyn as well these days. That is a lot easier compared to the fortran code. Have a look at the tutorial, part 2B.

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10 years 10 months ago #1600 by martini
Replied by martini on topic ElNeDyn tutorial
I am not sure to understand. I would like to compute a martini simulation without lost b-sheet structure. For that I use ELNEDYN approach . But you said that in martini.py elnedyn is already use so what is the aim of elnedyn???

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10 years 10 months ago #1601 by djurre
Replied by djurre on topic ElNeDyn tutorial
I understand the confusion. Elnedyn is largely the same forcefield as Martini with an elastic network and a few additional changes (backbone bead are at Calpha position iso COM, etc). The non-bonded interactions are exactly the same in both cases.

You can use the martinize.py script to create protein topologies using the Martini forcefield without Elastic network or the Martini+elastic network+additional small differences. The second case is the Elnedyn approach/setup.

(You could also create a Martini topology with elastic network but without the additional changes belonging to Elnedyn. This would be Martini with Elastic network. However this has nog been as extensively tested as the Elnedyn approach).

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10 years 10 months ago #1602 by martini
Replied by martini on topic ElNeDyn tutorial
Hi,

I read the tutorial which allow us to use Martini + elastic network but do you know how to use the option -elastic -ef -el -eu -ea -ep?? Which value you have to use???

When you use this option and we compute a production run as previous tuto the secondary structure have to be conserved???


THanks a lot .

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10 years 10 months ago #1603 by djurre
Replied by djurre on topic ElNeDyn tutorial
Are you sure you read the tutorial? It says:

"This turns on the elastic network (-elastic), sets the elastic bond force constant to 500 kJ mol-1 nm-2 (-ef 500), the lower and upper elastic bond cut-o to 0.5 and 0.9 nm, respectively, (-el 0.5 -eu 0.9) and makes the bond strengths independent of the bond length (elastic bond decay factor and decay power, -ea 0 -ep 0, respectively; these are default). The elastic network is defined in the .itp file by an "ifdef" statement (have a look!). The "#define RUBBER BANDS" in the .top or .itp file switches it on. Note that martinize.py does not generate elastic bonds between i->i+1 and i->i+2 backbone bonds, as those are already connected by bonds and angles."

In addition an example line, with values you can use, is given. But as I said before, these example values have not been tested extensively. Elnedyn (later in the tutorial) has been tested much more extensively. There the values a well established. So maybe you should use those.

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10 years 10 months ago #1604 by martini
Replied by martini on topic ElNeDyn tutorial
I am sorry I am really confused with this elastic Network.

So this part is in a way more "secure" :

"ElNeDyn

The second option to use elastic networks in combination with Martini puts more emphasis on remaining close to the overall structure as deposited in the PDB than standard Martini does. The main difference from the standard way (used in the previous exercise) is the use of a global elastic network between the backbone beads to conserve the conformation instead of relying on the
angle/dihedral potentials and/or local elastic bonds to do the job. The position of the backbone beads is also slightly dierent. In standard Martinithe center-of-mass of the peptide plane is used as the location of the backbone bead, but in the elastic network implementation the positions of the C-atoms are used for this.

The martinize.py script automatically sets these options and sets the correct parameters for the elastic network. As the elastic bondstrength and the upper cut-off have to be tuned in an ElNeDyn network, these options can be set manually (-ef -eu).

1. Use the martinize.py script to generate the coarse grain structure and topology as above. Set the following options:

-elnedyn -ef 500 -eu 0.9

This selects the ElNeDyn topology options, with a force constant of 500 kJ mol-1nm-2 (-ef 500) and an upper bond length cut-o of 0.9 nm (-eu 0.9)."

BUt , I am sorry to ask you again question, we can use this value "-elnedyn -ef 500 -eu 0.9" or we have to adapt this values our system??

THanks a lot

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10 years 10 months ago #1605 by djurre
Replied by djurre on topic ElNeDyn tutorial
Yes, it is probably more secure to use Elnedyn.

martini wrote: BUt , I am sorry to ask you again question, we can use this value "-elnedyn -ef 500 -eu 0.9" or we have to adapt this values our system??


No problem in asking again! I'm sorry I didn't asnwer it the first time:-)

In the Elnedyn article* they looked at different systems with different values for -ef and -eu. These values were pretty good for all system. You could optimize it for you protein, however this would involve doing a atomistic simulation first and then trying multiple values and check which one does best.

Since this is a lot of work and the gain is minimal, in practice we always use the current values.

*X. Periole, M. Cavalli, S.J. Marrink, M.A. Ceruso, Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition, J. Chem. Theory Comput., 5, 2531-2543 (2009)

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10 years 10 months ago #1606 by martini
Replied by martini on topic ElNeDyn tutorial
Thank you very much for taking the time to answer me.
Now it is much clearer ;)

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10 years 10 months ago #1607 by martini
Replied by martini on topic ElNeDyn tutorial
I am sorry last question:

I compute the simulation with option -elnedyn -ef 500 -eu 0.9 when I running martini.py after I did the same step of a last tutorial:

- editconf for obtain a gro file
- genbox for solvatation of the box
- add number of resname W in top file

and when I would like to compute a minimization I obtain this error:

Fatal error:
number of coordinates in coordinate file (solvated.gro, 9209)
does not match topology (system.top, 0)

But I add the water in top file:

#include "./martini_v2.1.itp"

#define RUBBER_BANDS

#include "Protein_A.itp"

[ system ]
; name
Martini system from cg.pdb

[ molecules ]
; name number
Protein_A 1
W 8926

Do you have an idea of whats happen??

I use this command: "grompp -f min.mdp -c solvated.gro -p system.top -o min1"

THanks a lot again

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10 years 10 months ago #1608 by xavier
Replied by xavier on topic ElNeDyn tutorial
That is a strange behaviour ... it seems grompp does not read your system.top file ... the file itself looks fine to me!

martini wrote: I am sorry last question:

I compute the simulation with option -elnedyn -ef 500 -eu 0.9 when I running martini.py after I did the same step of a last tutorial:

- editconf for obtain a gro file
- genbox for solvatation of the box
- add number of resname W in top file

and when I would like to compute a minimization I obtain this error:

Fatal error:
number of coordinates in coordinate file (solvated.gro, 9209)
does not match topology (system.top, 0)

But I add the water in top file:

#include "./martini_v2.1.itp"

#define RUBBER_BANDS

#include "Protein_A.itp"

[ system ]
; name
Martini system from cg.pdb

[ molecules ]
; name number
Protein_A 1
W 8926

Do you have an idea of whats happen??

I use this command: "grompp -f min.mdp -c solvated.gro -p system.top -o min1"

THanks a lot again

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10 years 10 months ago #1609 by martini
Replied by martini on topic ElNeDyn tutorial
Very strange, perhaps there is something wrong in my mdp file:

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)o


I have no idea of what I have to do .

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10 years 10 months ago #1610 by xavier
Replied by xavier on topic ElNeDyn tutorial
No this error tells that grompp does not read the system.top file correctly ... there is not other option ... check the file

martini wrote: Very strange, perhaps there is something wrong in my mdp file:

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)o


I have no idea of what I have to do .

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10 years 10 months ago #1611 by martini
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:o

I am so sorry its just a big STUPID error. I don't read correctly the error.
JUst above the error of coordinate there is this error :

"system.top:1:30: erreur fatale: ./martini_v2.1.itp : Aucun fichier ou dossier de ce type"

I completly forgot to change the name of the itp file .

I am really sorry

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10 years 10 months ago #1612 by xavier
Replied by xavier on topic ElNeDyn tutorial
That happens to all of us :)) Good you find you!

But you work on a french computer ... where are you?

Bonne chance!

martini wrote: :o

I am so sorry its just a big STUPID error. I don't read correctly the error.
JUst above the error of coordinate there is this error :

"system.top:1:30: erreur fatale: ./martini_v2.1.itp : Aucun fichier ou dossier de ce type"

I completly forgot to change the name of the itp file .

I am really sorry

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10 years 10 months ago #1613 by martini
Replied by martini on topic ElNeDyn tutorial
THis error can make people crazy :p

I am in Helsinki for my studie but I am french :p

Merci beaucoup pour votre aide :)

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10 years 10 months ago #1614 by xavier
Replied by xavier on topic ElNeDyn tutorial
Tu travailles avec qui? Le monde est petit ... :))

martini wrote: THis error can make people crazy :p

I am in Helsinki for my studie but I am french :p

Merci beaucoup pour votre aide :)

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10 years 10 months ago #1615 by martini
Replied by martini on topic ElNeDyn tutorial
Avec Dr ALex Bunker.

Me dis pas que tu es à Helsinki???

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10 years 10 months ago #1616 by xavier
Replied by xavier on topic ElNeDyn tutorial
Non je suis a Groningen :))

Bonne courage et a bientôt ..

martini wrote: Avec Dr ALex Bunker.

Me dis pas que tu es à Helsinki???

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10 years 10 months ago #1617 by martini
Replied by martini on topic ElNeDyn tutorial
Merci encore pour ton aide ;)

A bientôt.

PS: je m'appel Nawel et non martini :p ( faut que je change ça :p )

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