[gmx-users] please, how edr data is xdr packed?

[Alan Wilter Sousa da Silva]

Hi there,

I am trying to use python xdrlib module to read edr files but not knowing
how the data is packed using the xdr protocol makes my work very difficult,
if not impossible.

Would someone kindly tell me how data is packed in the edr file? Or where it
is the gromacs code so I can try to figure out a way?

I've read http://tools.ietf.org/html/rfc1832.html and for reference, see
topic "6. AN EXAMPLE OF AN XDR DATA DESCRIPTION".

My other option would be using a parsing code to read g_energy output but
this seems very silly.

Many thanks in advance,

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Re: [gmx-users] please, how edr data is xdr packed?

[David van der Spoel]

On 2010-08-22 13.14, Alan Wilter Sousa da Silva wrote:

Hi there,

I am trying to use python xdrlib module to read edr files but not
knowing how the data is packed using the xdr protocol makes my work very
difficult, if not impossible.

src/gmxlib/enxio.c


Would someone kindly tell me how data is packed in the edr file? Or
where it is the gromacs code so I can try to figure out a way?

I've read http://tools.ietf.org/html/rfc1832.html and for reference, see
topic "6. AN EXAMPLE OF AN XDR DATA DESCRIPTION".

My other option would be using a parsing code to read g_energy output
but this seems very silly.

Many thanks in advance,

Alan

--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
 >>http://www.bio.cam.ac.uk/~awd28<<




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] Does anyone know how to get the file charmm_gromacs.tar.gz?

[Michael McGovern]

I'm looking for an rtp file for charmm in gromacs and according 
to http://www.gromacs.org/Downloads/User_contributions/Other_softwareIt should 
be available in a file called charmm_gromacs.tar.gz 
athttp://www.gromacs.org/old/topologies/uploaded_force_fields/charmm_gromacs.tar.gz but
 the link is broken and just leads to the main gromacs web page.  Does anyone 
know where I can find this file, or maybe you have it yourself?Thanks a lot.


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Re: [gmx-users] Does anyone know how to get the file charmm_gromacs.tar.gz?

[David van der Spoel]

On 2010-08-22 15.16, Michael McGovern wrote:

I'm looking for an rtp file for charmm in gromacs and according to
http://www.gromacs.org/Downloads/User_contributions/Other_software
It should be available in a file called charmm_gromacs.tar.gz at
http://www.gromacs.org/old/topologies/uploaded_force_fields/charmm_gromacs.tar.gz

but the link is broken and just leads to the main gromacs web page. Does
anyone know where I can find this file, or maybe you have it yourself?
Thanks a lot.



Try the 4.5beta. It contains the charmm ff.

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] Metallic boundary conditions

[pojeda]

Hi,

I want to use metallic boundary conditions in my problem.
I think one can do that with the option epsilon_r =0 in gromacs.
If I set epsilon_r =0 I get the output:

Starting 2 threads
Making 1D domain decomposition 2 x 1 x 1
starting mdrun 'Dipoles'
1000 steps,   5000.0 ps.
Segmentation fault

With other values of epsilon (epsilon=1) the script works well.

and the .log file says:

Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 3.33e-07
Initial temperature: 300.135 K

Started mdrun on node 0 Sun Aug 22 17:23:15 2010

   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
9.37218e+04   -5.17070e+020.0e+00nannan
Kinetic En.   Total Energy  Conserved En.Temperature Pres. DC (bar)
nannannannan   -5.57291e+02
 Pressure (bar)   Constr. rmsd
nannan

My question is how could I introduce the metallic boundary
conditions? The input file reads:


; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
;dt   = 0.00278089542
dt   = 0.0005
nsteps   = 1000
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1000
; group(s) for center of mass motion removal
comm-grps=


; OUTPUT CONTROL OPTIONS
; Checkpointing helps you continue after crashes
nstcheckpoint= 500
; Output frequency for energies to log file and energy file
nstlog   = 1000
nstenergy= 1000
; Output frequency and precision for xtc file
nstxout  =1000
nstvout  =1000
nstfout  =1000

nstxtcout= 1000
xtc-precision= 10
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps   =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off
rlist= 0.9


;SOLVENT
implicit_solvent = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = pme
rcoulomb-switch  = 0
rcoulomb = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r= 0
;epsilon-rf= 0
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch  = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Spacing for the PME/PPPM FFT grid
;fourierspacing   = 0.07
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 32
fourier_ny   = 32
fourier_nz   = 32
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = yes



; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl   = nose-hoover
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 300.788

; Pressure coupling
;Pcoupl   = berendsen
;Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
;tau_p= 0.1
;compressibility  = 4.5e-5
;ref_p= 2.0


; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = yes
gen_temp = 300.788
gen_seed = -1

; OPTIONS FOR BONDS
constraints  = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
unconstrained-start  = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR= no
; Relative tolerance of shake
shake-tol= 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve ener

Re: [gmx-users] Metallic boundary conditions

[Florian Dommert]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1



On 08/22/2010 05:29 PM, poj...@icp.uni-stuttgart.de wrote:
> Hi,
> 
> I want to use metallic boundary conditions in my problem.
> I think one can do that with the option epsilon_r =0 in gromacs.
> If I set epsilon_r =0 I get the output:
> 

Metallic boundries are set with epsilon_surface=0

/Flo

> Starting 2 threads
> Making 1D domain decomposition 2 x 1 x 1
> starting mdrun 'Dipoles'
> 1000 steps,   5000.0 ps.
> Segmentation fault
> 
> With other values of epsilon (epsilon=1) the script works well.
> 
> and the .log file says:
> 
> Constraining the coordinates at t0-dt (step 0)
> RMS relative constraint deviation after constraining: 3.33e-07
> Initial temperature: 300.135 K
> 
> Started mdrun on node 0 Sun Aug 22 17:23:15 2010
> 
>Step   Time Lambda
>   00.00.0
> 
>Energies (kJ/mol)
> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
> 9.37218e+04   -5.17070e+020.0e+00nannan
> Kinetic En.   Total Energy  Conserved En.Temperature Pres. DC (bar)
> nannannannan   -5.57291e+02
>  Pressure (bar)   Constr. rmsd
> nannan
> 
> My question is how could I introduce the metallic boundary
> conditions? The input file reads:
> 
> 
> ; RUN CONTROL PARAMETERS
> integrator   = md
> ; Start time and timestep in ps
> tinit= 0
> ;dt   = 0.00278089542
> dt   = 0.0005
> nsteps   = 1000
> ; For exact run continuation or redoing part of a run
> init_step= 0
> ; mode for center of mass motion removal
> comm-mode= Linear
> ; number of steps for center of mass motion removal
> nstcomm  = 1000
> ; group(s) for center of mass motion removal
> comm-grps=
> 
> 
> ; OUTPUT CONTROL OPTIONS
> ; Checkpointing helps you continue after crashes
> nstcheckpoint= 500
> ; Output frequency for energies to log file and energy file
> nstlog   = 1000
> nstenergy= 1000
> ; Output frequency and precision for xtc file
> nstxout  =1000
> nstvout  =1000
> nstfout  =1000
> 
> nstxtcout= 1000
> xtc-precision= 10
> ; This selects the subset of atoms for the xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps =
> ; Selection of energy groups
> energygrps   =
> 
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist  = 10
> ; ns algorithm (simple or grid)
> ns_type  = grid
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc  = xyz
> ; nblist cut-off
> rlist= 0.9
> 
> 
> ;SOLVENT
> implicit_solvent = no
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype  = pme
> rcoulomb-switch  = 0
> rcoulomb = 0.9
> ; Dielectric constant (DC) for cut-off or DC of reaction field
> epsilon-r= 0
> ;epsilon-rf= 0
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> ; cut-off lengths
> rvdw-switch  = 0
> rvdw = 0.9
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension  = 1
> ; Spacing for the PME/PPPM FFT grid
> ;fourierspacing   = 0.07
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx   = 32
> fourier_ny   = 32
> fourier_nz   = 32
> ; EWALD/PME/PPPM parameters
> pme_order= 6
> ewald_rtol   = 1e-05
> ewald_geometry   = 3d
> epsilon_surface  = 0
> optimize_fft = yes
> 
> 
> 
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl   = nose-hoover
> ; Groups to couple separately
> tc-grps  = System
> ; Time constant (ps) and reference temperature (K)
> tau_t= 0.1
> ref_t= 300.788
> 
> ; Pressure coupling
> ;Pcoupl   = berendsen
> ;Pcoupltype   = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> ;tau_p= 0.1
> ;compressibility  = 4.5e-5
> ;ref_p= 2.0
> 
> 
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel  = yes
> gen_temp = 300.788
> gen_seed = -1
> 
> ; OPTIONS FOR BONDS
> constraints  = all-bonds
> ; Type of constraint algorithm
> constraint-algorithm 

[gmx-users] Metallic boundary conditions

[pojeda]

Hi,

thank you for your answer. What is then epsilon_r ?

regards.

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[gmx-users] Charmm to Gromacs: Polyols force field

[Eudes Fileti]

Olá pessoal,

Recently, McKerrel published his CHARMM force field to polyols (JCTC, 2009,
5, 1315).
I am very interested in using it in GROMACS.

For this, I began the transfer of the parameters with the following recipe:

1) All atom types were added to the atomtypes.atp file;
2) All bonded parameters (bonds, angles, ub, dihedral and impropers)
were added to the ffbonded.itp file;
3) van der Waals and Coulomb parameters were inserted properly
in ffnonbonded.itp;
4) The residues were created in a new file named polyols.rtp.

Well, pdb2gmx works fine! It generates the restraints file (posre.itp),
configuration file
(conf.gro) and topology file (topol.itp).  But when I run it in grommp, the
default for
parameters are not found. Something like:

ERROR 6 [file topol.top, line 40]:
  No default Bond types

I know I can insert the parameters by hand in each .top file generated by
pdb2gmx.
But what I need to do, so that grompp recognizes the default values
automatically.

Did I forgot some file? I'm making some mistake?

Any suggestion is welcome!

Muito obrigado!
eef

___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4996-0196
http://fileti.ufabc.edu.br
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Re: [gmx-users] Charmm to Gromacs: Polyols force field

[Justin A. Lemkul]

Eudes Fileti wrote:
Olá pessoal, 

Recently, McKerrel published his CHARMM force field to polyols (JCTC, 
2009, 5, 1315). 
I am very interested in using it in GROMACS.


For this, I began the transfer of the parameters with the following recipe:

1) All atom types were added to the atomtypes.atp file;
2) All bonded parameters (bonds, angles, ub, dihedral and impropers)
were added to the ffbonded.itp file;
3) van der Waals and Coulomb parameters were inserted properly
in ffnonbonded.itp;
4) The residues were created in a new file named polyols.rtp.

Well, pdb2gmx works fine! It generates the restraints file (posre.itp), 
configuration file 
(conf.gro) and topology file (topol.itp).  But when I run it in grommp, 
the default for 
parameters are not found. Something like:


ERROR 6 [file topol.top, line 40]:
  No default Bond types

I know I can insert the parameters by hand in each .top file generated 
by pdb2gmx. 
But what I need to do, so that grompp recognizes the default values 
automatically.


Did I forgot some file? I'm making some mistake?



Look on line 40 of the topology and see which atoms grompp is complaining about. 
 You likely forgot to define the parameters for that particular bond type.


-Justin


Any suggestion is welcome!

Muito obrigado!
eef

___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4996-0196
http://fileti.ufabc.edu.br



--


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


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[gmx-users] PMF

[abdul wadood]

Hi, All

I am trying to calculate pmf for enzyme ligand complex using the tutorial of 
umbrella sampling.
I have successfully created the unit cell around the protein and have solvated. 
The ions were also added by genion.
But when I run the minimization step with the command
grompp -f minim.mdp -c solv_ions.gro -p 3JY0.top -o em.tpr
the following error comes


Fatal error:
Molecule type 'NA+' contains no atoms


I tried my best to solve the problem but could no succeeded.
Any help to solve this problem will be highly appreciated. 
The topology file is attached.

Thanks in advace

Many regards

Abdul Wadood, 
Research Scholar, 
Dr.Panjwani Center for Molecular Medicine and 
Drug Research, 
International Center for Chemical and 
Biological Science, 
University of Karachi, Karachi-75720, Pakistan. 
Email:wadoodbiochem...@hotmail.com 


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