Re: [gmx-users] velocity autocorrelation function.

[David van der Spoel]

On 2010-06-03 08.23, #ZHAO LINA# wrote:

Hi,

When I looked up the manual about the autocorrelation (Chapter 8.5. Correlation 
functions). There is a very general (simple) descriptions. I feel I need a bit 
more deep-relevant references.
gmx_velacc.c (g_velacc) which computes the velocity autocorrelation function, 
it's really hard for me to read such a nice codes.
If I want to know much more about the specific formula of velocity 
autocorrelation functions which is being used in gromacs and how it's 
implemented, which way I should go?

Great appreciation for any advice,

Best Regards,

lina
This is described quite well in the textbook by Allen adn Tildesley 
(1987) you will find the reference in the manual.


--
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] velocity autocorrelation function.

[#ZHAO LINA#]

Hi,

When I looked up the manual about the autocorrelation (Chapter 8.5. Correlation 
functions). There is a very general (simple) descriptions. I feel I need a bit 
more deep-relevant references.
gmx_velacc.c (g_velacc) which computes the velocity autocorrelation function, 
it's really hard for me to read such a nice codes.
If I want to know much more about the specific formula of velocity 
autocorrelation functions which is being used in gromacs and how it's 
implemented, which way I should go?

Great appreciation for any advice,

Best Regards,

lina
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Re: [gmx-users] CG (MARTINI) parameters for RNA

[Itamar Kass]

Hi Tom,

Thanks for your replay. From the paper (DNA and lipid bilayers: 
self-assembly and insertion. J. Royal Soc. Int. 5, S241-S250, 2008. ) I 
understand that the DNA CG particles where identical to the one used for 
lipids and protein, am I correct? Also, they had used elastic network to 
hold them in place (instead of Secondary Structure used in proteins).


Best,
Itamar

On 28/05/10 12:11 AM, Thomas Piggot wrote:

Hi,

The DNA parameters for use with the MARTINI forcefield are not 
publicly available to download at the moment, however they will be 
available very soon. I (or someone else from the Khalid group) will 
let the list know when and where they have been made available.


Cheers

Tom

Itamar Kass wrote:

Shalom all,

I wish to try and simulate a protein with few RNA bases attached. As I
favour speed over accuracy in this case I wish to use the MARTINI model.
I could not find RNA/DNA parameters, but noticed that on the site there
is a reference to Khalid S, Bond PJ, Holyoake J, Hawtin RW, Sansom MSP.
DNA and lipid bilayers: self-assembly and insertion. J. Royal Soc. Int.
  5, S241-S250, 2008.

I wonder if someone had those parameters already implemented into the
model? It will be nice to get it nicely packed. Or maybe even better,
are there any beta parameters to RNA/DNA in a new MARTINI force field?

All the best,
Itamar





--


"In theory, there is no difference between theory and practice. But, in practice, 
there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu.au


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[gmx-users] I know about improper dihedrals (i.e. gi_1) , etc. Is there a way to keep phenyl rings absolutely flat.

[Arthur Roberts]

Hi, all,

I need to keep a molecule absolutely flat. I know about improper  
dihedrals (i.e. gi_1), but it doesn't seem to be enough to keep it  
flat.  It seems to get bent a little bit.  I have a system with a  
phenyl ring and protons and I am trying to run GROMOS 96 ff53a6 force  
field.  I appreciate your ideas.


Much appreciated,
Art

Dr. Arthur Roberts, Ph.D.
University of California, San Diego
Skaggs School of Pharmacy and Pharmaceutical Sciences
9500 Gilman Drive #0703
La Jolla, CA 92093-0703

email: aroberts99...@yahoo.com
cell: 206-850-7468
skype=aroberts92122



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[gmx-users] Discrete structure factor from g_rdf

[comcon1]

> On 02.06.2010, at 09:37, comc...@erg.biophys.msu.ru wrote:
>
>> I'm trying to repeat some X-ray diffraction analysis on lipid bilayers
>> according to the article:
>>
>> http://dx.doi.org/10.1529/biophysj.104.046821 (it's free)
>>
>> I have several corrected OPLS all-atom bilayer models and I need to
>> validate my model according to experimental x-ray diffraction data. But
>> I
>> can't understand, how '-sq' property of g_rdf can helps me to compute
>> structure factor.. May be anybody have some experience in this theme?
>>
>
>  So far I also haven't really used g_rdf to calculate the structure factor
> of a system, so I can't give you a hint how to reproduce the results in
> the paper. However as the version of g_rdf in the current and earlier
> release was not able to treat every atomtype perhaps you should at first
> consider the git version of g_rdf for your calculations. This version is
> capable of treating every atomtype if you supply the corresponding data.
> The calculation is based on a so called Cromer-Mann fit that requires
> different parameters for different atoms. This parameters can be for
> example obtained from
>
> http://www.ruppweb.org/xray/comp/scatfac.htm
>
> There is a reference to an article and a short introduction contained on
> the website.
>
> Finally append your parameters to the list in share/top/sfactor.dat and
> use the corresponding flag in the command line ( g_rdf -h will tell you
> which)
>
> /Flo

Thx for ans!

I have already done this. I also modify sfactor.c a little to select atoms
acording to atom number instead of atom name ;-) But `g_rdf -sd` gives me
plot of 'absorbtion units' versus 'reverse nanometers'. And it looks
absolutely different from structure factor from article I cited. For
example in article SF is fading sinusoid while g_rdf gives me positive
increasing curve. I suppose it's diffraction spectrum, not structure
factor. Or ... ?

(i rly have no idea, so i'm scanning source code of sfactor.c now, but may
be anybody know what `g_rdf -sd` exactly do?? )

Thanx before,
comcon1)




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Re: [gmx-users] PBC

[ms]

On 02/06/10 18:48, Morteza Khabiri wrote:

Dear users

I have a dimer protein in the water box. It was run for 30ns.
during the simulation dimer split to two monomer. This things happen bc of
PBC. ( I checked it by vmd pbc option )
to have a two monomer together during trajectories (for visualization)
I have used the following command:

trjconv  -s .tpr -f .xtc -o   -boxcenter tric -pbc mol

but it is not working.


Not working *how*? that is, what is output? .tpr and .xtc don't look 
like sensible file parameters.



Is there any other method or command which I could implement pbc in
trajectory.

Thanks in advance

Morteza



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[gmx-users] PBC

[Morteza Khabiri]

Dear users

I have a dimer protein in the water box. It was run for 30ns.
during the simulation dimer split to two monomer. This things happen bc of
PBC. ( I checked it by vmd pbc option )
to have a two monomer together during trajectories (for visualization)
I have used the following command:

trjconv  -s .tpr -f .xtc -o   -boxcenter tric -pbc mol

but it is not working.
Is there any other method or command which I could implement pbc in
trajectory.

Thanks in advance

Morteza

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Re: [gmx-users] Position restraint for 2ns

[Justin A. Lemkul]

Rabab Toubar wrote:

Hi,

I am trying to reproduce some steps from a  paper, the authors set 
position restraint to the protein (all-bonds) with a force constant of 
1000 for 2ns.


Constraints and restraints are different things in Gromacs, so setting position 
restraints is done independently of constraining bond lengths.


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

I edited the pr.md file  where nsteps would result in 2 ns, and I 
searched the mailing list and knew that the force cons is 1000 by 
default if we define -DPOSRES
My question is the run ended very quickly that doesn't seem 2ns for me. 
I apologize if it is a silly question but I have just strated using GMX

Thanks


Well, what does the log file say?  What does gmxcheck tell you about your 
trajectory and/or energy files?  I don't know what you mean by saying it 
"doesn't seem" like your trajectory is complete.  GROMACS is known for begin fast :)


-Justin



Rabab Toubar




--


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


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Re: [gmx-users] Strange bilayer behavior in protein-multimembrane models

[Justin A. Lemkul]

Thomas Schmidt wrote:

Dear all,

by doing MD simulations of a protein complex embedded in 2 membranes
(inner and outer membrane of bacteria, POPE), we observe a bilayer
splitting in one of the membranes. This has the effect that the bilayer
forms "bubbles" with vacuum inside.



We have seen this before with POPE membranes, which appear to be particularly 
problematic.  We solved it by using a better equilibration protocol that 
involved simulated annealing (from a very low temperature up to 310 K).  For us, 
it seemed to happen independently of just about anything we tried.


-Justin


It might have something to do with the PME handling of GroMACS 4.0.3
(GROMOS96-53a6 ff).
- there is no splitting using a 1 nm smaller boxsize in exactly the same
model
- if we switch off the PME mode and use only Cut-off's we don't have
any splitting effect
- the behavior of the bilayer splitting depends on the number of used
cluster/cpu nodes

Changing the "fourierspacing" parameter to create different PME grids
has no effect to avoid bilayer splitting.

Changing: thermostat | barostat (semiisotropic):
- berendsen | berendsen: "splitting"
- v-rescale | parrinello-rahman: "splitting"/"keep together" (50:50)


Here's the mdp file of our last try:
title   = Yep, sometimes I will cause a bilayer splitting;

; The following lines tell the program the standard locations where to
find certain files
cpp = cpp; Preprocessor
include = -I../top; Directories to include in the topology
format
define  = -DPOSRES; Apply position restraints.



; RUN CONTROL PARAMETERS
integrator   = MD
; Start time and timestep in ps
tinit= 0
dt   = 0.002
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  = 1
; group(s) for center of mass motion removal
comm-grps= Protein POPE_center POPE_inner POPE_outer
SOL_NA+_CL-



; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 500
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 0
; Step size (1/ps^2) for minimization of flexible constraints
fcstep   = 0



; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 50
nstvout  = 50
nstfout  = 0
; Checkpointing helps you continue after crashes
nstcheckpoint= 5
; Output frequency for energies to log file and energy file
nstlog   = 5000
nstenergy= 5000
; Output frequency and precision for xtc file
nstxtcout= 5
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = Protein POPE_center POPE_inner POPE_outer
SOL_NA+_CL-
; Selection of energy groups
energygrps   = Protein POPE_center POPE_inner POPE_outer
SOL_NA+_CL-



; 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= 1.15
domain-decomposition = no



; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.15
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r= 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch  = 0
rvdw = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = yes



; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
; Tcoupl   = berendsen
Tcoupl   = V-rescale
; Groups to couple separately
tc-grps  = Protein POPE_center POPE_inner POPE_outer
SOL_NA+_CL-
; Time constant (ps) and reference temperature (K)
tau-t= 0.1 0.1 0.1 0.1 0.1
ref-t= 310 31

[gmx-users] Position restraint for 2ns

[Rabab Toubar]

Hi,

I am trying to reproduce some steps from a  paper, the authors set position 
restraint to the protein (all-bonds) with a force constant of 1000 for 2ns.
I edited the pr.md file  where nsteps would result in 2 ns, and I searched the 
mailing list and knew that the force cons is 1000 by default if we define 
-DPOSRES
My question is the run ended very quickly that doesn't seem 2ns for me. I 
apologize if it is a silly question but I have just strated using GMX
Thanks

Rabab Toubar



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Re: [gmx-users] RE:Range checking error

[Justin A. Lemkul]

lloyd riggs wrote:

Dear All,

Before I start, I have already searched through the mailing list archives, 
etc...and have energy minimized my structure (s) ;

I get the range check error;
_
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 19683 ]
__

does anyone have a fix for this?  


I have first energy minimized my structures.  There are two seperate proteins 
with two seperate protein domains (chain a,b each) making up two receptors 
which interact with eachother transiently, or strongly in the presence of a 
molecule.  The two proteins are seperated (manually) by 10 angstroms.

I first energy minimized these, then added waters and ions.  I had problems 
with force fields that recognized all the ions (Mg2+, Ca2+, K+, Na+, Cl-) and 
ended up using the oplsaa force fields.

Now, I try an initial run, MD or a simple 100 step energy minimization, prior 
to a long run, and get the above error again and again.  The two scripts 
mentioned are below inline.  I have however played around with everything I 
could.  I have also started from scratch 3 times, ie the initial 
proteins-minimize-add waters/ions-and then it crashes?

Also, does anyone know what the variable "ci" is?  





integrator = md 
dt = 0.005 


With a timestep of 5 fs, you should (at minimum) be using constraints, and 
probably virtual sites as well.  Does a more sensible timestep (like 1 or 2 fs) 
make your system stable?


nsteps = 1000 
nstxout = 10 
nstvout = 10 
nstlog = 1000 
nstenergy = 1000 
nstxtcout = 1000 
xtc_grps = system 
energygrps = system 
nstlist = 20 


You should aim for an nstlist that will update your neighborlist roughly every 
10-20 ps, or else (in theory) you could be missing interactions.  With your 
neighborlist updated every 100 ps (!) then your short-range interactions could 
be changing quite a bit.


coulombtype = PME 
ns_type = grid 
rlist = 1.5 
rcoulomb = 1.5 
rvdw = 1.5 
pbc = xyz 
table-extension = 20


;Temperature coupling 
tcoupl  = berendsen
tc-grps = system 


Coupling the whole system in one temperature bath may or may not be appropriate. 
 Although not the most likely culprit for your problem, you should be aware. 
See here, particularly the cited references:


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


tau_t = 1.0
ref_t = 50.0 


; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
Pcoupltype  =  isotropic
tau_p   =  2.01
compressibility =  4.5e-5
ref_p   =  1.0
refcoord_scaling=  all

;Velocity generation 
gen_vel = yes 
gen_temp = 50.0 
gen_seed = 30 
ld_seed = 130 
comm_mode = angular 



In a periodic system, using this comm_mode is inappropriate.  Surely grompp 
warned you about this?


-Justin


--


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


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[gmx-users] Strange bilayer behavior in protein-multimembrane models

[Thomas Schmidt]

Dear all,

by doing MD simulations of a protein complex embedded in 2 membranes
(inner and outer membrane of bacteria, POPE), we observe a bilayer
splitting in one of the membranes. This has the effect that the bilayer
forms "bubbles" with vacuum inside.

It might have something to do with the PME handling of GroMACS 4.0.3
(GROMOS96-53a6 ff).
- there is no splitting using a 1 nm smaller boxsize in exactly the same
model
- if we switch off the PME mode and use only Cut-off's we don't have
any splitting effect
- the behavior of the bilayer splitting depends on the number of used
cluster/cpu nodes

Changing the "fourierspacing" parameter to create different PME grids
has no effect to avoid bilayer splitting.

Changing: thermostat | barostat (semiisotropic):
- berendsen | berendsen: "splitting"
- v-rescale | parrinello-rahman: "splitting"/"keep together" (50:50)


Here's the mdp file of our last try:
title   = Yep, sometimes I will cause a bilayer splitting;

; The following lines tell the program the standard locations where to
find certain files
cpp = cpp; Preprocessor
include = -I../top; Directories to include in the topology
format
define  = -DPOSRES; Apply position restraints.



; RUN CONTROL PARAMETERS
integrator   = MD
; Start time and timestep in ps
tinit= 0
dt   = 0.002
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  = 1
; group(s) for center of mass motion removal
comm-grps= Protein POPE_center POPE_inner POPE_outer
SOL_NA+_CL-



; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 500
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 0
; Step size (1/ps^2) for minimization of flexible constraints
fcstep   = 0



; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 50
nstvout  = 50
nstfout  = 0
; Checkpointing helps you continue after crashes
nstcheckpoint= 5
; Output frequency for energies to log file and energy file
nstlog   = 5000
nstenergy= 5000
; Output frequency and precision for xtc file
nstxtcout= 5
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = Protein POPE_center POPE_inner POPE_outer
SOL_NA+_CL-
; Selection of energy groups
energygrps   = Protein POPE_center POPE_inner POPE_outer
SOL_NA+_CL-



; 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= 1.15
domain-decomposition = no



; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.15
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r= 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch  = 0
rvdw = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = yes



; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
; Tcoupl   = berendsen
Tcoupl   = V-rescale
; Groups to couple separately
tc-grps  = Protein POPE_center POPE_inner POPE_outer
SOL_NA+_CL-
; Time constant (ps) and reference temperature (K)
tau-t= 0.1 0.1 0.1 0.1 0.1
ref-t= 310 310 310 310 310
; Pressure coupling
; Pcoupl   = berendsen
Pcoupl   = Parrinello-Rahman
Pcoupltype   = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p= 4 4
compressibility  = 4.5e-5 4.5e-5
ref-p= 1.0 1.0
; Random

Re: [gmx-users] Discrete structure factor from g_rdf

[Florian Dommert]

On 02.06.2010, at 09:37, comc...@erg.biophys.msu.ru wrote:

> I'm trying to repeat some X-ray diffraction analysis on lipid bilayers
> according to the article:
> 
> http://dx.doi.org/10.1529/biophysj.104.046821 (it's free)
> 
> I have several corrected OPLS all-atom bilayer models and I need to
> validate my model according to experimental x-ray diffraction data. But I
> can't understand, how '-sq' property of g_rdf can helps me to compute
> structure factor.. May be anybody have some experience in this theme?
> 

 So far I also haven't really used g_rdf to calculate the structure factor of a 
system, so I can't give you a hint how to reproduce the results in the paper. 
However as the version of g_rdf in the current and earlier release was not able 
to treat every atomtype perhaps you should at first consider the git version of 
g_rdf for your calculations. This version is capable of treating every atomtype 
if you supply the corresponding data. The calculation is based on a so called 
Cromer-Mann fit that requires different parameters for different atoms. This 
parameters can be for example obtained from 

http://www.ruppweb.org/xray/comp/scatfac.htm

There is a reference to an article and a short introduction contained on the 
website.

Finally append your parameters to the list in share/top/sfactor.dat and use the 
corresponding flag in the command line ( g_rdf -h will tell you which)

/Flo 
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[gmx-users] RE:Range checking error

[lloyd riggs]

Dear All,

Before I start, I have already searched through the mailing list archives, 
etc...and have energy minimized my structure (s) ;

I get the range check error;
_
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 19683 ]
__

does anyone have a fix for this?  

I have first energy minimized my structures.  There are two seperate proteins 
with two seperate protein domains (chain a,b each) making up two receptors 
which interact with eachother transiently, or strongly in the presence of a 
molecule.  The two proteins are seperated (manually) by 10 angstroms.

I first energy minimized these, then added waters and ions.  I had problems 
with force fields that recognized all the ions (Mg2+, Ca2+, K+, Na+, Cl-) and 
ended up using the oplsaa force fields.

Now, I try an initial run, MD or a simple 100 step energy minimization, prior 
to a long run, and get the above error again and again.  The two scripts 
mentioned are below inline.  I have however played around with everything I 
could.  I have also started from scratch 3 times, ie the initial 
proteins-minimize-add waters/ions-and then it crashes?

Also, does anyone know what the variable "ci" is?  

Thanks for any help

Stephan Watkins

Energy minimize short;

title   =  
cpp = 
define  =
constraints =  none
integrator  =  steep
tinit   =  0
dt  =  0.002; ps !
nsteps  =  100
init_step   =  0

;
;   Energy minimizing stuff
;
emtol   =  100.0
emstep  =  0.02
__
energy minimize long;


constraints =  all-bonds
integrator  =  cg
dt  =  0.002; ps !
nsteps  =  100
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
 ;
 ;   Energy minimizing stuff
 ;
 emtol   =  1000.0
 emstep  =  0.01
nstcgsteep  =  25
__
and  the MD run file;

 
integrator = md 
dt = 0.005 
nsteps = 1000 
nstxout = 10 
nstvout = 10 
nstlog = 1000 
nstenergy = 1000 
nstxtcout = 1000 
xtc_grps = system 
energygrps = system 
nstlist = 20 
coulombtype = PME 
ns_type = grid 
rlist = 1.5 
rcoulomb = 1.5 
rvdw = 1.5 
pbc = xyz 
table-extension = 20

;Temperature coupling 
tcoupl  = berendsen
tc-grps = system 
tau_t = 1.0
ref_t = 50.0 

; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
Pcoupltype  =  isotropic
tau_p   =  2.01
compressibility =  4.5e-5
ref_p   =  1.0
refcoord_scaling=  all

;Velocity generation 
gen_vel = yes 
gen_temp = 50.0 
gen_seed = 30 
ld_seed = 130 
comm_mode = angular 

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Re: [gmx-users] question about compass ff

[David van der Spoel]

On 6/2/10 2:40 PM, Justin A. Lemkul wrote:



Andrei Neamtu wrote:

Justin, thank you.

In fact I am worried about the cross coupling terms which apper i the
functional form of COMPASS and CVFF.

As far as I know in GROMACS there are no such terms, so I am asking if
there might be a solution to include these by editing .itp, nb.itp,
bon.itp, .rtp, etc, without the need to modify the gromacs CODE.



These are very complicated functional forms, indeed. You may be able to
use tabulated bonded potentials, but I don't have much experience in
that arena, so I don't know if even that would be possible.



Have you checked the manual? There are some cross coupling functions for 
bonds/angles. I don't know what Compass wants though.



-Justin


Andrei

On Wed, Jun 2, 2010 at 2:23 PM, Justin A. Lemkul  wrote:


Andrei Neamtu wrote:

Dear all,

does anyone know if it is possible to somehow use COMPASS or CVFF
forcefields in Gromacs?


You can probably implement just about anything by creating the right
files
(.itp, nb.itp, bon.itp, .rtp, etc). Quite a bit of work, but not too
conceptually difficult. Whether or not there need to be changes to the
source code to accommodate new force fields may be another issue.

-Justin


Thanks,
Andrei

--


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


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Re: [gmx-users] question about compass ff

[Justin A. Lemkul]

Andrei Neamtu wrote:

Justin, thank you.

In fact I am worried about the cross coupling terms which apper i the
functional form of COMPASS and CVFF.

As far as I know in GROMACS there are no such terms, so I am asking if
there might be a solution to include these by editing .itp, nb.itp,
bon.itp, .rtp, etc, without the need to modify the gromacs CODE.



These are very complicated functional forms, indeed.  You may be able to use 
tabulated bonded potentials, but I don't have much experience in that arena, so 
I don't know if even that would be possible.


-Justin


Andrei

On Wed, Jun 2, 2010 at 2:23 PM, Justin A. Lemkul  wrote:


Andrei Neamtu wrote:

Dear all,

does anyone know if it is possible to somehow use COMPASS or CVFF
forcefields in Gromacs?


You can probably implement just about anything by creating the right files
(.itp, nb.itp, bon.itp, .rtp, etc).  Quite a bit of work, but not too
conceptually difficult.  Whether or not there need to be changes to the
source code to accommodate new force fields may be another issue.

-Justin


Thanks,
Andrei

--


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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--


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


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Re: [gmx-users] question about compass ff

[Andrei Neamtu]

Justin, thank you.

In fact I am worried about the cross coupling terms which apper i the
functional form of COMPASS and CVFF.

As far as I know in GROMACS there are no such terms, so I am asking if
there might be a solution to include these by editing .itp, nb.itp,
bon.itp, .rtp, etc, without the need to modify the gromacs CODE.

Andrei

On Wed, Jun 2, 2010 at 2:23 PM, Justin A. Lemkul  wrote:
>
>
> Andrei Neamtu wrote:
>>
>> Dear all,
>>
>> does anyone know if it is possible to somehow use COMPASS or CVFF
>> forcefields in Gromacs?
>>
>
> You can probably implement just about anything by creating the right files
> (.itp, nb.itp, bon.itp, .rtp, etc).  Quite a bit of work, but not too
> conceptually difficult.  Whether or not there need to be changes to the
> source code to accommodate new force fields may be another issue.
>
> -Justin
>
>> Thanks,
>> Andrei
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] question about compass ff

[Justin A. Lemkul]

Andrei Neamtu wrote:

Dear all,

does anyone know if it is possible to somehow use COMPASS or CVFF
forcefields in Gromacs?



You can probably implement just about anything by creating the right files 
(.itp, nb.itp, bon.itp, .rtp, etc).  Quite a bit of work, but not too 
conceptually difficult.  Whether or not there need to be changes to the source 
code to accommodate new force fields may be another issue.


-Justin


Thanks,
Andrei


--


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] Instantenous Hessian Matrix

[Sebastian Waltz]

Hi all,

is there a way to get the hessian matrix for each time step
for which I also print out the trr? Or do I have to run
normal mode analysis for each configuration?


Thanks a lot
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Re: [gmx-users] water clusters MD

[Oleksandr]

In addition to Marks e-mail and in order to close the topic I suggest you to 
exempt people from your "mentor" comments in future.

O.

--- On Wed, 6/2/10, Mark Abraham  wrote:

> From: Mark Abraham 
> Subject: Re: [gmx-users] water clusters MD
> To: "Discussion list for GROMACS users" 
> Date: Wednesday, June 2, 2010, 9:52 AM
> - Original Message -
> From: Oleksandr 
> Date: Wednesday, June 2, 2010 13:12
> Subject: Re: [gmx-users] water clusters MD
> To: Mark Abraham 
> 
> > There is some  inconsistency between the top/itp
> files that 
> > you provided.
> > The grompp gives an error "Found a second defaults
> directive."
> 
> Please do not take discussions off the list. See 
> http://www.gromacs.org/Support for why.
> 
> My suggested files are not inconsistent. I have only one
> such directive and there's no way to get a second one
> without you doing something wrong. I can't have any idea
> what's happened since, and you haven't bothered to tell me.
> This particular error occurs regularly with new users, and
> is discussed here http://www.gromacs.org/Documentation/Errors.
> 
> This goes to prove my point that you need more general
> experience of GROMACS before tackling this specific problem.
> Learn to walk before assuming you can run!
> 
> Mark
> --
> gmx-users mailing list    gmx-users@gromacs.org
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> 




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Re: Re: Re: [gmx-users] “Fatal error in PMP I_Bcast: Other MPI error, …..” occurs whe n using the ‘particle decomposition’ option.

[xhomes]

Ok, thanks for the comments! I
think I will conduct the simulation with ‘constraints=hbonds’, since I had 
done so in NAMD. I guess it wouldn't bring big
problem to the trajectory except increasing the compute cost. - 
Original Message -From: xho...@sohu.comdate: Wednesday, June 2, 2010 
14:17Subject:  Re:  Re: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI 
error, …..” occurs when using the ‘particle decomposition’ option.To: 
Discussion list for GROMACS users > Hi, Mark,  
>    > I’ve noticed about the minimum cell diameter restrict, but I 
still had no idea about how to adjust the related parameter after I read the 
manual part mentioned by the error info. I don’t have too much understanding 
about the algorithm, so I turned around to rely on the ‘-pd’ option:)OK, but my 
point is that if you know you need constraints=all-bonds, then you need a 
bigger system before GROMACS will be able to parallelise it.  >    > 
About choosing double precision, I notice normal mode analysis need the double 
precision version of some programs. And I don’t know whether I should use 
double precision version of mdrun for covariance analysis, so I just chose the 
double one! Sure, doing EM in double is standard advice for preparing for NMA.  
> I also don’t have too much idea about choosing which ensemble to conduct 
covariance analysis. I’ve noticed that temperature coupling would ‘correct’ the 
motion of the atoms. I think a more ‘natural’ trajectory with least artifact 
should be generated for covariance analysis. Any comments about this?One 
"always" wants accurate thermodynamic sampling of the target ensemble. What 
ensemble to target depends mostly on your simulation objective. NPT usually 
makes the most sense for comparision with experimental data. You should read up 
on the algorithms that regulate T and P to see what the wisest choices may be 
with respect to accurate sampling, because there are sound reasons for one 
choice or another. Start with the GROMACS manual.Mark-- -- 
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Re: Re: Re: [gmx-users] “Fatal err or in PMPI_Bcast: Other MPI error, …..” oc curs when using the ‘particle decomposition’ optio n.

[Mark Abraham]

- Original Message -
From: xho...@sohu.com
Date: Wednesday, June 2, 2010 14:17
Subject:  Re:  Re: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI error, 
…..” occurs when using the ‘particle decomposition’ option.
To: Discussion list for GROMACS users 

> Hi, Mark,
  >  
  > I’ve noticed about the minimum cell diameter restrict, but I still had no 
idea about how to adjust the related parameter after I read the manual part 
mentioned by the error info. I don’t have too much understanding about the 
algorithm, so I turned around to rely on the ‘-pd’ option:)
OK, but my point is that if you know you need constraints=all-bonds, then you 
need a bigger system before GROMACS will be able to parallelise it.

  >  
  > About choosing double precision, I notice normal mode analysis need the 
double precision version of some programs. And I don’t know whether I should 
use double precision version of mdrun for covariance analysis, so I just chose 
the double one! 

Sure, doing EM in double is standard advice for preparing for NMA.

  > I also don’t have too much idea about choosing which ensemble to conduct 
covariance analysis. I’ve noticed that temperature coupling would ‘correct’ the 
motion of the atoms. I think a more ‘natural’ trajectory with least artifact 
should be generated for covariance analysis. Any comments about this?
One "always" wants accurate thermodynamic sampling of the target ensemble. What 
ensemble to target depends mostly on your simulation objective. NPT usually 
makes the most sense for comparision with experimental data. You should read up 
on the algorithms that regulate T and P to see what the wisest choices may be 
with respect to accurate sampling, because there are sound reasons for one 
choice or another. Start with the GROMACS manual.

Mark

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Re: [gmx-users] number of water molecules affects the PMF

[XAvier Periole]

On Jun 2, 2010, at 9:49 AM, Ozge Engin wrote:


Hi Chris,

The two setups were different from each other in terms of only the  
number of water molecules. Even the starting
conformations for the two peptides were the same. I especially took  
care about that to leave only the number of molecules as a variable.


I calculated the error by dividing the whole data to 4, and  
calculated the standard deviation between the 4 sets, and divided  
the result by sqrt (3).


For the Xavier's suggestion: I think I should wait a little, at  
least until having the same length of trajectory for the two sets.

Here we go! You are probably not converged! How long did you simulate?


Thanks

--
Ozge Engin
★☆
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Re: [gmx-users] water clusters MD

[Mark Abraham]

- Original Message -
From: Oleksandr 
Date: Wednesday, June 2, 2010 13:12
Subject: Re: [gmx-users] water clusters MD
To: Mark Abraham 

> There is some  inconsistency between the top/itp files that 
> you provided.
> The grompp gives an error "Found a second defaults directive."

Please do not take discussions off the list. See http://www.gromacs.org/Support 
for why.

My suggested files are not inconsistent. I have only one such directive and 
there's no way to get a second one without you doing something wrong. I can't 
have any idea what's happened since, and you haven't bothered to tell me. This 
particular error occurs regularly with new users, and is discussed here 
http://www.gromacs.org/Documentation/Errors.

This goes to prove my point that you need more general experience of GROMACS 
before tackling this specific problem. Learn to walk before assuming you can 
run!

Mark
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[gmx-users] Discrete structure factor from g_rdf

[comcon1]

I'm trying to repeat some X-ray diffraction analysis on lipid bilayers
according to the article:

http://dx.doi.org/10.1529/biophysj.104.046821 (it's free)

I have several corrected OPLS all-atom bilayer models and I need to
validate my model according to experimental x-ray diffraction data. But I
can't understand, how '-sq' property of g_rdf can helps me to compute
structure factor.. May be anybody have some experience in this theme?

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[gmx-users] number of water molecules affects the PMF

[Ozge Engin]

Hi Chris,

The two setups were different from each other in terms of only the number of
water molecules. Even the starting
conformations for the two peptides were the same. I especially took care
about that to leave only the number of molecules as a variable.

I calculated the error by dividing the whole data to 4, and calculated the
standard deviation between the 4 sets, and divided the result by sqrt (3).

For the Xavier's suggestion: I think I should wait a little, at least until
having the same length of trajectory for the two sets.

Thanks

-- 
Ozge Engin
★☆
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[gmx-users] question about compass ff

[Andrei Neamtu]

Dear all,

does anyone know if it is possible to somehow use COMPASS or CVFF
forcefields in Gromacs?

Thanks,
Andrei
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