Re: [gmx-users] Distance restraints exploding system

[Trayder Thomas]

To wrap this up for anyone who stumbles across this in the future:

The 'solution' I ended up going with was to avoid using hydrogen atoms in
the restraints, instead restraining to the e.g. methyl carbon and adding a
fudge factor to the restraint length to account for the C-H distance.
This results in slightly 'looser' restraints but actually runs stably.

-Trayder


On Tue, Sep 3, 2013 at 5:32 AM, Rafael I. Silverman y de la Vega <
rsilv...@ucsc.edu> wrote:

> Have you tried with even less restraints? I found systems are not always
> stable with more than the bare minimum of restraints
>
>
> On Sun, Sep 1, 2013 at 7:54 PM, Trayder Thomas  >wrote:
>
> > It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to
> have
> > an impact. I've tried being gentle, slowly turning up the force constant
> > and running for 1 ns for each value but as soon as the force constant
> > approaches 100 it crashes.
> > The starting structure was generated with the same restraints, so it is
> > very close. I have tried using slightly different starting structures as
> > well.
> >
> > I've tried running it with only 3 restraints (1 methyl group to 1
> hydrogen
> > with the restraints extended by 0.2nm so that all hydrogens are within
> the
> > restraint distance) and I'm getting a segmentation fault (no LINCS
> > warnings) at 100 steps. It runs fine with any combination of 2 hydrogens
> > restrained, but as soon as I restrain the 3rd one I get a segmentation
> > fault (this occurs with either setting for disre-weighting). So it seems
> to
> > fair better with more restraints?
> >
> > The more I try to solve this problem the less it makes sense!
> >
> > -Trayder
> >
> >
> > On Fri, Aug 30, 2013 at 6:02 PM, Mark Abraham  > >wrote:
> >
> > > On Fri, Aug 30, 2013 at 8:56 AM, Trayder 
> > > wrote:
> > > > Hello,
> > > > I am attempting to simulate a protein-ligand complex using distance
> > > > restraints to match it to NMR data.
> > > > The system runs stably without restraints. With restraints it tends
> to
> > > spit
> > > > out LINCS angle warnings and blow up under most conditions.
> > > >
> > > > I'm attempting to use:
> > > > ;   Restraints
> > > > disre   =  simple
> > > > disre-weighting =  conservative
> > > > disre-fc=  1000
> > > >
> > > > It blows up within 100 steps unless:
> > > > I run on a single core (+gpu) or
> > > > disre-fc = <100 or
> > > > disre-weighting = equal
> > > >
> > > > If disre-weighting = conservative is causing extreme forces, then I
> > > figure
> > > > it should do the same on 1 core.
> > >
> > > Not really. MD is chaotic. Small changes in initial conditions lead to
> > > different results.
> > >
> > > > If domain decomposition is the problem, then I would think
> > > disre-weighting =
> > > > equal shouldn't work either.
> > > > I'm stumped... anyone got any ideas?
> > >
> > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up has the
> > > usual suggestions - don't use P-R yet, try a smaller time step, make
> > > sure your system is close to the restrained regime (or be extra gentle
> > > until it is).
> > >
> > > Mark
> > >
> > > > Thanks in advance,
> > > > -Trayder
> > > >
> > > > Distance restraints excerpt:
> > > > ; aiaj  typeindex   type’   low up1 up2 fac
> > > > ; 2 symmetric hydrogens
> > > >  1306  1389 1   10  1   0.0 0.548   1.0 1.0
> > > >  1306  1396 1   10  1   0.0 0.548   1.0 1.0
> > > > ; Diastereotopic methyl groups
> > > >  1306  1374 1   11  1   0.0 0.654   1.0 1.0
> > > >  1306  1375 1   11  1   0.0 0.654   1.0 1.0
> > > >  1306  1376 1   11  1   0.0 0.654   1.0 1.0
> > > >  1306  1385 1   11  1   0.0 0.654   1.0 1.0
> > > >  1306  1386 1   11  1   0.0 0.654   1.0 1.0
> > > >  1306  1387 1   11  1   0.0 0.654   1.0 1.0
> > > >
> > > > Full mdp:
> > > > ;   Run Control
> > > > integrator  =  md  ; simulation algorithm
> > > > tinit= 0
> > > > dt   = 0.002
> > > > nsteps  =  50
> > > > ;
> > > > ;   Output Control
> > > > nstxout =  20; write coordinates
> to
> > > .trr
> > > > nstvout =  20; write velocities
> to
> > > .trr
> > > > nstlog  =  1000 ; write energies to
> > .log
> > > > nstenergy   =  4000 ; write energies to
> > .edr
> > > > nstxtcout   =  1000  ; write coordinates
> to
> > > .xtc
> > > > ;
> > > > ;   Neighbour Searching
> > > > nstlist =  10   ; update neighbour
> list
> > > > ns_type =  grid ; neighbour list
> method
> > > > pbc =  xyz  ; periodic boundary
>

Re: [gmx-users] Distance restraints exploding system

[Rafael I. Silverman y de la Vega]

Have you tried with even less restraints? I found systems are not always
stable with more than the bare minimum of restraints


On Sun, Sep 1, 2013 at 7:54 PM, Trayder Thomas wrote:

> It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have
> an impact. I've tried being gentle, slowly turning up the force constant
> and running for 1 ns for each value but as soon as the force constant
> approaches 100 it crashes.
> The starting structure was generated with the same restraints, so it is
> very close. I have tried using slightly different starting structures as
> well.
>
> I've tried running it with only 3 restraints (1 methyl group to 1 hydrogen
> with the restraints extended by 0.2nm so that all hydrogens are within the
> restraint distance) and I'm getting a segmentation fault (no LINCS
> warnings) at 100 steps. It runs fine with any combination of 2 hydrogens
> restrained, but as soon as I restrain the 3rd one I get a segmentation
> fault (this occurs with either setting for disre-weighting). So it seems to
> fair better with more restraints?
>
> The more I try to solve this problem the less it makes sense!
>
> -Trayder
>
>
> On Fri, Aug 30, 2013 at 6:02 PM, Mark Abraham  >wrote:
>
> > On Fri, Aug 30, 2013 at 8:56 AM, Trayder 
> > wrote:
> > > Hello,
> > > I am attempting to simulate a protein-ligand complex using distance
> > > restraints to match it to NMR data.
> > > The system runs stably without restraints. With restraints it tends to
> > spit
> > > out LINCS angle warnings and blow up under most conditions.
> > >
> > > I'm attempting to use:
> > > ;   Restraints
> > > disre   =  simple
> > > disre-weighting =  conservative
> > > disre-fc=  1000
> > >
> > > It blows up within 100 steps unless:
> > > I run on a single core (+gpu) or
> > > disre-fc = <100 or
> > > disre-weighting = equal
> > >
> > > If disre-weighting = conservative is causing extreme forces, then I
> > figure
> > > it should do the same on 1 core.
> >
> > Not really. MD is chaotic. Small changes in initial conditions lead to
> > different results.
> >
> > > If domain decomposition is the problem, then I would think
> > disre-weighting =
> > > equal shouldn't work either.
> > > I'm stumped... anyone got any ideas?
> >
> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up has the
> > usual suggestions - don't use P-R yet, try a smaller time step, make
> > sure your system is close to the restrained regime (or be extra gentle
> > until it is).
> >
> > Mark
> >
> > > Thanks in advance,
> > > -Trayder
> > >
> > > Distance restraints excerpt:
> > > ; aiaj  typeindex   type’   low up1 up2 fac
> > > ; 2 symmetric hydrogens
> > >  1306  1389 1   10  1   0.0 0.548   1.0 1.0
> > >  1306  1396 1   10  1   0.0 0.548   1.0 1.0
> > > ; Diastereotopic methyl groups
> > >  1306  1374 1   11  1   0.0 0.654   1.0 1.0
> > >  1306  1375 1   11  1   0.0 0.654   1.0 1.0
> > >  1306  1376 1   11  1   0.0 0.654   1.0 1.0
> > >  1306  1385 1   11  1   0.0 0.654   1.0 1.0
> > >  1306  1386 1   11  1   0.0 0.654   1.0 1.0
> > >  1306  1387 1   11  1   0.0 0.654   1.0 1.0
> > >
> > > Full mdp:
> > > ;   Run Control
> > > integrator  =  md  ; simulation algorithm
> > > tinit= 0
> > > dt   = 0.002
> > > nsteps  =  50
> > > ;
> > > ;   Output Control
> > > nstxout =  20; write coordinates to
> > .trr
> > > nstvout =  20; write velocities to
> > .trr
> > > nstlog  =  1000 ; write energies to
> .log
> > > nstenergy   =  4000 ; write energies to
> .edr
> > > nstxtcout   =  1000  ; write coordinates to
> > .xtc
> > > ;
> > > ;   Neighbour Searching
> > > nstlist =  10   ; update neighbour list
> > > ns_type =  grid ; neighbour list method
> > > pbc =  xyz  ; periodic boundary
> > > conditions
> > > rlist   =  0.9  ; cut-off for
> short-range
> > > neighbour (nm)
> > > cutoff-scheme   =  verlet
> > > ;
> > > ;   Electrostatics and VdW
> > > coulombtype =  PME  ; type of coulomb
> > > interaction
> > > rcoulomb=  0.9  ; cut-off distance for
> > > coulomb
> > > epsilon_r   =  1; dielectric constant
> > > rvdw=  0.9  ; cut-off for vdw
> > > fourierspacing  =  0.12 ; maximum grid spacing
> > for
> > > FFT
> > > pme_order   =  4; interpolation order
> f

Re: [gmx-users] Distance restraints exploding system

[Trayder Thomas]

It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have
an impact. I've tried being gentle, slowly turning up the force constant
and running for 1 ns for each value but as soon as the force constant
approaches 100 it crashes.
The starting structure was generated with the same restraints, so it is
very close. I have tried using slightly different starting structures as
well.

I've tried running it with only 3 restraints (1 methyl group to 1 hydrogen
with the restraints extended by 0.2nm so that all hydrogens are within the
restraint distance) and I'm getting a segmentation fault (no LINCS
warnings) at 100 steps. It runs fine with any combination of 2 hydrogens
restrained, but as soon as I restrain the 3rd one I get a segmentation
fault (this occurs with either setting for disre-weighting). So it seems to
fair better with more restraints?

The more I try to solve this problem the less it makes sense!

-Trayder


On Fri, Aug 30, 2013 at 6:02 PM, Mark Abraham wrote:

> On Fri, Aug 30, 2013 at 8:56 AM, Trayder 
> wrote:
> > Hello,
> > I am attempting to simulate a protein-ligand complex using distance
> > restraints to match it to NMR data.
> > The system runs stably without restraints. With restraints it tends to
> spit
> > out LINCS angle warnings and blow up under most conditions.
> >
> > I'm attempting to use:
> > ;   Restraints
> > disre   =  simple
> > disre-weighting =  conservative
> > disre-fc=  1000
> >
> > It blows up within 100 steps unless:
> > I run on a single core (+gpu) or
> > disre-fc = <100 or
> > disre-weighting = equal
> >
> > If disre-weighting = conservative is causing extreme forces, then I
> figure
> > it should do the same on 1 core.
>
> Not really. MD is chaotic. Small changes in initial conditions lead to
> different results.
>
> > If domain decomposition is the problem, then I would think
> disre-weighting =
> > equal shouldn't work either.
> > I'm stumped... anyone got any ideas?
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up has the
> usual suggestions - don't use P-R yet, try a smaller time step, make
> sure your system is close to the restrained regime (or be extra gentle
> until it is).
>
> Mark
>
> > Thanks in advance,
> > -Trayder
> >
> > Distance restraints excerpt:
> > ; aiaj  typeindex   type’   low up1 up2 fac
> > ; 2 symmetric hydrogens
> >  1306  1389 1   10  1   0.0 0.548   1.0 1.0
> >  1306  1396 1   10  1   0.0 0.548   1.0 1.0
> > ; Diastereotopic methyl groups
> >  1306  1374 1   11  1   0.0 0.654   1.0 1.0
> >  1306  1375 1   11  1   0.0 0.654   1.0 1.0
> >  1306  1376 1   11  1   0.0 0.654   1.0 1.0
> >  1306  1385 1   11  1   0.0 0.654   1.0 1.0
> >  1306  1386 1   11  1   0.0 0.654   1.0 1.0
> >  1306  1387 1   11  1   0.0 0.654   1.0 1.0
> >
> > Full mdp:
> > ;   Run Control
> > integrator  =  md  ; simulation algorithm
> > tinit= 0
> > dt   = 0.002
> > nsteps  =  50
> > ;
> > ;   Output Control
> > nstxout =  20; write coordinates to
> .trr
> > nstvout =  20; write velocities to
> .trr
> > nstlog  =  1000 ; write energies to .log
> > nstenergy   =  4000 ; write energies to .edr
> > nstxtcout   =  1000  ; write coordinates to
> .xtc
> > ;
> > ;   Neighbour Searching
> > nstlist =  10   ; update neighbour list
> > ns_type =  grid ; neighbour list method
> > pbc =  xyz  ; periodic boundary
> > conditions
> > rlist   =  0.9  ; cut-off for short-range
> > neighbour (nm)
> > cutoff-scheme   =  verlet
> > ;
> > ;   Electrostatics and VdW
> > coulombtype =  PME  ; type of coulomb
> > interaction
> > rcoulomb=  0.9  ; cut-off distance for
> > coulomb
> > epsilon_r   =  1; dielectric constant
> > rvdw=  0.9  ; cut-off for vdw
> > fourierspacing  =  0.12 ; maximum grid spacing
> for
> > FFT
> > pme_order   =  4; interpolation order for
> > PME
> > ewald_rtol  =  1e-5 ; relative strength of
> > Ewald-shifted
> > DispCorr=  EnerPres ; long range dispersion
> > corrections
> > ;
> > ;   Restraints
> > disre   =  simple
> > disre-weighting =  conservative
> > disre-fc=  1000
> > ;
> > ;   Temperature Coupling
> > Tcoupl  =  v-rescale; type 

Re: [gmx-users] Distance restraints exploding system

[Mark Abraham]

On Fri, Aug 30, 2013 at 8:56 AM, Trayder  wrote:
> Hello,
> I am attempting to simulate a protein-ligand complex using distance
> restraints to match it to NMR data.
> The system runs stably without restraints. With restraints it tends to spit
> out LINCS angle warnings and blow up under most conditions.
>
> I'm attempting to use:
> ;   Restraints
> disre   =  simple
> disre-weighting =  conservative
> disre-fc=  1000
>
> It blows up within 100 steps unless:
> I run on a single core (+gpu) or
> disre-fc = <100 or
> disre-weighting = equal
>
> If disre-weighting = conservative is causing extreme forces, then I figure
> it should do the same on 1 core.

Not really. MD is chaotic. Small changes in initial conditions lead to
different results.

> If domain decomposition is the problem, then I would think disre-weighting =
> equal shouldn't work either.
> I'm stumped... anyone got any ideas?

http://www.gromacs.org/Documentation/Terminology/Blowing_Up has the
usual suggestions - don't use P-R yet, try a smaller time step, make
sure your system is close to the restrained regime (or be extra gentle
until it is).

Mark

> Thanks in advance,
> -Trayder
>
> Distance restraints excerpt:
> ; aiaj  typeindex   type’   low up1 up2 fac
> ; 2 symmetric hydrogens
>  1306  1389 1   10  1   0.0 0.548   1.0 1.0
>  1306  1396 1   10  1   0.0 0.548   1.0 1.0
> ; Diastereotopic methyl groups
>  1306  1374 1   11  1   0.0 0.654   1.0 1.0
>  1306  1375 1   11  1   0.0 0.654   1.0 1.0
>  1306  1376 1   11  1   0.0 0.654   1.0 1.0
>  1306  1385 1   11  1   0.0 0.654   1.0 1.0
>  1306  1386 1   11  1   0.0 0.654   1.0 1.0
>  1306  1387 1   11  1   0.0 0.654   1.0 1.0
>
> Full mdp:
> ;   Run Control
> integrator  =  md  ; simulation algorithm
> tinit= 0
> dt   = 0.002
> nsteps  =  50
> ;
> ;   Output Control
> nstxout =  20; write coordinates to .trr
> nstvout =  20; write velocities to .trr
> nstlog  =  1000 ; write energies to .log
> nstenergy   =  4000 ; write energies to .edr
> nstxtcout   =  1000  ; write coordinates to .xtc
> ;
> ;   Neighbour Searching
> nstlist =  10   ; update neighbour list
> ns_type =  grid ; neighbour list method
> pbc =  xyz  ; periodic boundary
> conditions
> rlist   =  0.9  ; cut-off for short-range
> neighbour (nm)
> cutoff-scheme   =  verlet
> ;
> ;   Electrostatics and VdW
> coulombtype =  PME  ; type of coulomb
> interaction
> rcoulomb=  0.9  ; cut-off distance for
> coulomb
> epsilon_r   =  1; dielectric constant
> rvdw=  0.9  ; cut-off for vdw
> fourierspacing  =  0.12 ; maximum grid spacing for
> FFT
> pme_order   =  4; interpolation order for
> PME
> ewald_rtol  =  1e-5 ; relative strength of
> Ewald-shifted
> DispCorr=  EnerPres ; long range dispersion
> corrections
> ;
> ;   Restraints
> disre   =  simple
> disre-weighting =  conservative
> disre-fc=  1000
> ;
> ;   Temperature Coupling
> Tcoupl  =  v-rescale; type of temperature
> coupling
> tc-grps =  Protein non-Protein   ; coupled
> groups
> tau_t   =  .1 .1   ; T-coupling time
> constant (ps)
> ref_t   =  310 310  ; reference temperature
> (K)
> ;
> ;   Pressure Coupling
> Pcoupl  =  parrinello-rahman; type of pressure
> coupling
> Pcoupltype  =  isotropic; pressure coupling geometry
> tau_p   =  2.0 ; p-coupling time constant
> (ps)
> compressibility =  4.5e-5   ; compressibiity
> ref_p   =  1.0  ; reference pressure (bar)
> ;
> ;   Velocity Generation
> gen_vel =  no   ; generate initial
> velocities
> ;
> ;   Bonds
> constraints =  all-bonds; which bonds to contrain
> constraint_algorithm= lincs ; algorithm to use
> lincs_order =  4
> lincs_iter =  2
>
>
>
>
>
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/Distance-restraints-exploding-system-tp5010842.html
> Sent from the GROMACS Users Forum 

[gmx-users] Distance restraints exploding system

[Trayder]

Hello,
I am attempting to simulate a protein-ligand complex using distance
restraints to match it to NMR data.
The system runs stably without restraints. With restraints it tends to spit
out LINCS angle warnings and blow up under most conditions.

I'm attempting to use:
;   Restraints
disre   =  simple
disre-weighting =  conservative
disre-fc=  1000

It blows up within 100 steps unless:
I run on a single core (+gpu) or
disre-fc = <100 or
disre-weighting = equal 

If disre-weighting = conservative is causing extreme forces, then I figure
it should do the same on 1 core.
If domain decomposition is the problem, then I would think disre-weighting =
equal shouldn't work either.
I'm stumped... anyone got any ideas?

Thanks in advance,
-Trayder

Distance restraints excerpt:
; aiaj  typeindex   type’   low up1 up2 fac
; 2 symmetric hydrogens 
 1306  1389 1   10  1   0.0 0.548   1.0 1.0
 1306  1396 1   10  1   0.0 0.548   1.0 1.0
; Diastereotopic methyl groups 
 1306  1374 1   11  1   0.0 0.654   1.0 1.0
 1306  1375 1   11  1   0.0 0.654   1.0 1.0
 1306  1376 1   11  1   0.0 0.654   1.0 1.0
 1306  1385 1   11  1   0.0 0.654   1.0 1.0
 1306  1386 1   11  1   0.0 0.654   1.0 1.0
 1306  1387 1   11  1   0.0 0.654   1.0 1.0

Full mdp:
;   Run Control
integrator  =  md  ; simulation algorithm
tinit= 0
dt   = 0.002
nsteps  =  50
;
;   Output Control
nstxout =  20; write coordinates to .trr
nstvout =  20; write velocities to .trr
nstlog  =  1000 ; write energies to .log
nstenergy   =  4000 ; write energies to .edr
nstxtcout   =  1000  ; write coordinates to .xtc
;
;   Neighbour Searching
nstlist =  10   ; update neighbour list
ns_type =  grid ; neighbour list method
pbc =  xyz  ; periodic boundary
conditions
rlist   =  0.9  ; cut-off for short-range
neighbour (nm)
cutoff-scheme   =  verlet
;
;   Electrostatics and VdW
coulombtype =  PME  ; type of coulomb
interaction
rcoulomb=  0.9  ; cut-off distance for
coulomb
epsilon_r   =  1; dielectric constant
rvdw=  0.9  ; cut-off for vdw
fourierspacing  =  0.12 ; maximum grid spacing for
FFT
pme_order   =  4; interpolation order for
PME
ewald_rtol  =  1e-5 ; relative strength of
Ewald-shifted
DispCorr=  EnerPres ; long range dispersion
corrections
;
;   Restraints
disre   =  simple
disre-weighting =  conservative
disre-fc=  1000
;
;   Temperature Coupling
Tcoupl  =  v-rescale; type of temperature
coupling
tc-grps =  Protein non-Protein   ; coupled
groups
tau_t   =  .1 .1   ; T-coupling time
constant (ps)
ref_t   =  310 310  ; reference temperature
(K)
;
;   Pressure Coupling
Pcoupl  =  parrinello-rahman; type of pressure
coupling
Pcoupltype  =  isotropic; pressure coupling geometry
tau_p   =  2.0 ; p-coupling time constant
(ps)
compressibility =  4.5e-5   ; compressibiity
ref_p   =  1.0  ; reference pressure (bar)
;
;   Velocity Generation
gen_vel =  no   ; generate initial
velocities
;
;   Bonds
constraints =  all-bonds; which bonds to contrain
constraint_algorithm= lincs ; algorithm to use
lincs_order =  4
lincs_iter =  2





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Re: [gmx-users] Distance restraints

[Justin Lemkul]

On 5/21/13 12:53 PM, Rama Krishna Koppisetti wrote:

Hi..,Mark

but it is within the same molecule , not in inter-molecules.



That's what distance restraints are designed for.  Please refer to the manual 
for topology syntax and explanation of the relevant parameters.


-Justin





On Tue, May 21, 2013 at 11:36 AM, Mark Abraham wrote:


Yes. Check out the manual first!

Mark


On Tue, May 21, 2013 at 5:16 PM, Rama Krishna Koppisetti <
ramkishn...@gmail.com> wrote:


Hi Mark,

Is there anyway to define NMR distance restraints in MD simulations to do
refinement for the complex structure.





On Tue, May 21, 2013 at 10:11 AM, Mark Abraham 
wrote:



You can't - the atoms must be part of the same [moleculetype]. The good
news is that a [moleculetype] can have whatever you want in it, so you

can

have more than one molecule. The bad news is that you'll have to be

cunning

with renumbering atoms in the merged [moleculetype] and there's no

tools

that do that. (Or maybe there's a smart-alec trick using the pull code,

but

I have no idea what.)

Mark


On Tue, May 21, 2013 at 4:20 PM, Rama  wrote:



Dear Gromacs users,

How to define distance restraints between two molecules(protein and a
lipid)
in a topology file.


Thanks..



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Re: [gmx-users] Distance restraints

[Rama Krishna Koppisetti]

Hi..,Mark

but it is within the same molecule , not in inter-molecules.




On Tue, May 21, 2013 at 11:36 AM, Mark Abraham wrote:

> Yes. Check out the manual first!
>
> Mark
>
>
> On Tue, May 21, 2013 at 5:16 PM, Rama Krishna Koppisetti <
> ramkishn...@gmail.com> wrote:
>
> > Hi Mark,
> >
> > Is there anyway to define NMR distance restraints in MD simulations to do
> > refinement for the complex structure.
> >
> >
> >
> >
> >
> > On Tue, May 21, 2013 at 10:11 AM, Mark Abraham  > >wrote:
> >
> > > You can't - the atoms must be part of the same [moleculetype]. The good
> > > news is that a [moleculetype] can have whatever you want in it, so you
> > can
> > > have more than one molecule. The bad news is that you'll have to be
> > cunning
> > > with renumbering atoms in the merged [moleculetype] and there's no
> tools
> > > that do that. (Or maybe there's a smart-alec trick using the pull code,
> > but
> > > I have no idea what.)
> > >
> > > Mark
> > >
> > >
> > > On Tue, May 21, 2013 at 4:20 PM, Rama  wrote:
> > >
> > > >
> > > > Dear Gromacs users,
> > > >
> > > > How to define distance restraints between two molecules(protein and a
> > > > lipid)
> > > > in a topology file.
> > > >
> > > >
> > > > Thanks..
> > > >
> > > >
> > > >
> > > > --
> > > > View this message in context:
> > > > http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.html
> > > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > > > --
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Re: [gmx-users] Distance restraints

[Mark Abraham]

Yes. Check out the manual first!

Mark


On Tue, May 21, 2013 at 5:16 PM, Rama Krishna Koppisetti <
ramkishn...@gmail.com> wrote:

> Hi Mark,
>
> Is there anyway to define NMR distance restraints in MD simulations to do
> refinement for the complex structure.
>
>
>
>
>
> On Tue, May 21, 2013 at 10:11 AM, Mark Abraham  >wrote:
>
> > You can't - the atoms must be part of the same [moleculetype]. The good
> > news is that a [moleculetype] can have whatever you want in it, so you
> can
> > have more than one molecule. The bad news is that you'll have to be
> cunning
> > with renumbering atoms in the merged [moleculetype] and there's no tools
> > that do that. (Or maybe there's a smart-alec trick using the pull code,
> but
> > I have no idea what.)
> >
> > Mark
> >
> >
> > On Tue, May 21, 2013 at 4:20 PM, Rama  wrote:
> >
> > >
> > > Dear Gromacs users,
> > >
> > > How to define distance restraints between two molecules(protein and a
> > > lipid)
> > > in a topology file.
> > >
> > >
> > > Thanks..
> > >
> > >
> > >
> > > --
> > > View this message in context:
> > > http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.html
> > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > > --
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Re: [gmx-users] Distance restraints

[Rama Krishna Koppisetti]

Hi Mark,

Is there anyway to define NMR distance restraints in MD simulations to do
refinement for the complex structure.





On Tue, May 21, 2013 at 10:11 AM, Mark Abraham wrote:

> You can't - the atoms must be part of the same [moleculetype]. The good
> news is that a [moleculetype] can have whatever you want in it, so you can
> have more than one molecule. The bad news is that you'll have to be cunning
> with renumbering atoms in the merged [moleculetype] and there's no tools
> that do that. (Or maybe there's a smart-alec trick using the pull code, but
> I have no idea what.)
>
> Mark
>
>
> On Tue, May 21, 2013 at 4:20 PM, Rama  wrote:
>
> >
> > Dear Gromacs users,
> >
> > How to define distance restraints between two molecules(protein and a
> > lipid)
> > in a topology file.
> >
> >
> > Thanks..
> >
> >
> >
> > --
> > View this message in context:
> > http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
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> >
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Re: [gmx-users] Distance restraints

[Mark Abraham]

You can't - the atoms must be part of the same [moleculetype]. The good
news is that a [moleculetype] can have whatever you want in it, so you can
have more than one molecule. The bad news is that you'll have to be cunning
with renumbering atoms in the merged [moleculetype] and there's no tools
that do that. (Or maybe there's a smart-alec trick using the pull code, but
I have no idea what.)

Mark


On Tue, May 21, 2013 at 4:20 PM, Rama  wrote:

>
> Dear Gromacs users,
>
> How to define distance restraints between two molecules(protein and a
> lipid)
> in a topology file.
>
>
> Thanks..
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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[gmx-users] Distance restraints

[Rama]

Dear Gromacs users,

How to define distance restraints between two molecules(protein and a lipid)
in a topology file.


Thanks..



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[gmx-users] Distance Restraints

[Rama]

Hi,

I'm new to Gromacs. How to convert NMR paramagnetic relaxation enhancement
distance restraints into gromacs format in topol.top file for structural MD
refinement.


--Rama



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Re: [gmx-users] Distance restraints

[Justin Lemkul]

On 2/14/13 8:35 AM, Divya Sunil wrote:

Hello all,

I have been trying to apply distance restraints on my protein. I prepared
distance restrains using make index and added to topology file. I did it
just after executing pdb2gmx. Is this the correct procedure to apply
distance restraints?



make_ndx doesn't produce restraints, but if you used an index file as input into 
genrestr -disre, then that's probably correct.  The disre.itp file that will be 
produced will be very generic, with the same restraint distances for everything, 
so that may or may not be correct for whatever it is you're trying to do.  It's 
easy to manually edit, of course.  Bottom line is that a simple test simulation 
and subsequent measurements will tell you if it is working properly.


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] distance restraints around Zn atom

[Mark Abraham]

On 26/07/2012 3:27 PM, Priyanka Shah wrote:

Dear all,

I want to apply distance restraint between Zn and its coordinating
atoms. Zn is supposed to be in octahedral geometry. Zn is making
coordination bond with O of hydroxyl group in ligand atom also. Even
after several attempts, it seems like destance restraint is not
effective because after 1ns MD run, ligand and Zn both move away from
their position in opposite directions.

  I have put following lines in mdp file:

title   = Protein-ligand complex
define  = -DPOSRESLIG   ; distance restrain from metal
disre = simple


Distance restraints and position restraints are totally different 
things. It looks like you need to clean up your work flow in this regard.




and added following lines into .top file
; Include Position restraint file
#ifdef POSRESLIG
#include "metalposre.itp"
#endif

where metalporse.itp contains

   671 11637 1 3  1  0.09   0.192 0.291
   4059 11637 1 7  1   0.11   0.210.311
   4070 11637 110  1  0.096   0.196 0.296  1
   4071 11637 112  1  0.094   0.1950.295   1
11637 11662 114  1   0.12   0.230.32   1

where 671 -> OD2 of Asp45, 4059 -> NE2 of Hid267, 4070 -> OD1 of
Asp268, 4071 -> OD2 of Asp268, 11637 -> Zn and 11662 -> O of Lig.

looking for suggestions.


Your .log and .edr files will have contributions from restraint 
violations, which you can use as a necessary-but-not-sufficient test for 
things working correctly.


Mark
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[gmx-users] distance restraints around Zn atom

[Priyanka Shah]

Dear all,

I want to apply distance restraint between Zn and its coordinating
atoms. Zn is supposed to be in octahedral geometry. Zn is making
coordination bond with O of hydroxyl group in ligand atom also. Even
after several attempts, it seems like destance restraint is not
effective because after 1ns MD run, ligand and Zn both move away from
their position in opposite directions.

 I have put following lines in mdp file:

title   = Protein-ligand complex
define  = -DPOSRESLIG   ; distance restrain from metal
disre = simple

and added following lines into .top file
; Include Position restraint file
#ifdef POSRESLIG
#include "metalposre.itp"
#endif

where metalporse.itp contains

  671 11637 1 3  1  0.09   0.192 0.291
  4059 11637 1 7  1   0.11   0.210.311
  4070 11637 110  1  0.096   0.196 0.296  1
  4071 11637 112  1  0.094   0.1950.295   1
11637 11662 114  1   0.12   0.230.32   1

where 671 -> OD2 of Asp45, 4059 -> NE2 of Hid267, 4070 -> OD1 of
Asp268, 4071 -> OD2 of Asp268, 11637 -> Zn and 11662 -> O of Lig.

looking for suggestions.

Thank you

Priyanka Shah
Central Drug Research Institute
Lucknow, India
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[gmx-users] Distance Restraints of 3 atoms

[Steven Neumann]

Dear Gmx Users,

I want use distance restraints of 3 atoms belonging to 3 different
moleculetypes. In this case shall I create and index file of those atoms
and then use:

genrestr -f X.pdb -n index.ndx -disre -o disre.itp ?

Under which topology file shall I add:

#ifdef DISRES
# include 'disre.itp'

Please help,

Steven
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Re: [gmx-users] Distance restraints not working

[Justin A. Lemkul]

On 5/22/12 9:25 PM, Thomas Grant wrote:

Dear all,

I am attempting to keep a Zn ion in place in a zinc finger motif using distance
restraints to the coordinating cysteine residues.  The zinc is structural and
not catalytic, and it was suggested from this list that using distance
restraints should suffice without the need for reparameterization.

Unfortunately after several tries the distance restraints don't appear to be
applied after 100 ps of isothermal-isochoric equilibration, however it did seem
to work for the minimization step.  My topology file contains the following:

#ifdef DISRES
[ distance_restraints ]
; ai   aj   type index typeâ low up1 up2 fac
   13082 5576 10 1 0.0 0.23 0.3 1.0
   13082 5604 11 1 0.0 0.23 0.3 1.0
   13082 5959 12 1 0.0 0.23 0.3 1.0
   13082 5993 13 1 0.0 0.20 0.3 1.0
#endif

and my .mdp file has the following two lines inserted:

define  = -DDISRES  ; distance restrain the protein
disre   = simple; Enable Distance Restraints

I first attempted to use small factors to multiply the restraints, 1, 2, 10, but
nothing seemed to be working so I just put an extreme value of 10,000 to ensure
the energy contribution from the restraints would dominate and keep the zinc in
place, but that still didn't seem to do the trick which makes me think that
there's some other error I'm missing.  I checked my .gro file to ensure that the
atom indices were correct and they are.  I also have ensured that the zinc ion
and coordinating cysteines are part of the same chain. The zinc appears to move
by about 4 Å to be coordinated by a nearby glutamate instead.

Any ideas on why the restraints don't seem to be working?



There are a few possibilities.

1. Numbering in [distance_restraints] is not based on .gro numbering.  The atom 
numbers supplied are only relevant within the [moleculetype] to which they 
belong, much like [position_restraints].  Also make sure that the 
[distance_restraints] block is in the correct location in the topology.


2. You've omitted the dihre_fc keyword, though it is set to 1000 by default. 
Check the mdout.mdp file or your .tpr file to ensure that you have a sensible 
value here.  Setting values of fac that high are unnecessary.


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Distance restraints not working

[Thomas Grant]

Dear all,

I am attempting to keep a Zn ion in place in a zinc finger motif using
distance restraints to the coordinating cysteine residues.  The zinc is
structural and not catalytic, and it was suggested from this list that
using distance restraints should suffice without the need for
reparameterization.

Unfortunately after several tries the distance restraints don't appear to
be applied after 100 ps of isothermal-isochoric equilibration, however it
did seem to work for the minimization step.  My topology file contains the
following:

#ifdef DISRES
[ distance_restraints ]
; ai   aj   type index typeâ low up1 up2 fac
  13082 5576 10 1 0.0 0.23 0.3 1.0
  13082 5604 11 1 0.0 0.23 0.3 1.0
  13082 5959 12 1 0.0 0.23 0.3 1.0
  13082 5993 13 1 0.0 0.20 0.3 1.0
#endif

and my .mdp file has the following two lines inserted:

define  = -DDISRES  ; distance restrain the protein
disre   = simple; Enable Distance Restraints

I first attempted to use small factors to multiply the restraints, 1, 2,
10, but nothing seemed to be working so I just put an extreme value of
10,000 to ensure the energy contribution from the restraints would dominate
and keep the zinc in place, but that still didn't seem to do the trick
which makes me think that there's some other error I'm missing.  I checked
my .gro file to ensure that the atom indices were correct and they are.  I
also have ensured that the zinc ion and coordinating cysteines are part of
the same chain. The zinc appears to move by about 4 Å to be coordinated by
a nearby glutamate instead.

Any ideas on why the restraints don't seem to be working?

Thanks,
Tom


--
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Graduate Research Assistant
Hauptman-Woodward Medical Research Institute
700 Ellicott St.
Buffalo, NY 14203
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Re: [gmx-users] distance restraints

[Justin A. Lemkul]

On 5/17/12 2:51 AM, Banafsheh Mehrazma wrote:

Dear all
I 'd like to do NOE distance restraints;  according to the chapter 4 of the 
manual;
I should specify a section for [ distance_restraints] :

[ distance_restraints ]
; ai  aj  type  index  type’  low  up1  up2  fac
10   161010.00.30.41.0
10   281110.00.30.41.0
10   461110.00.30.41.0
16   221210.00.30.42.5
16   341310.00.50.61.0
.
althought I've studied the manual, it is still unclear to me, that how is the
index column defined? what are the numbers (0,1,2,3) implying? what about the
low, up1,up2, fac columns?



All of this information is in the manual, section 4.3.4, under the heading 
"Using distance restraints."


With respect to indices:

"The type column should always be 1. As explained in sec. 4.3.4, multiple 
distances can contribute to a single NOE signal. In the topology this can be set 
using the index column. In our example, the restraints 10-28 and 10-46 both have 
index 1, therefore they are treated simultaneously."


With respect to low, up1, and up2:

"The columns low, up1, and up2 hold the values of r0, r1, and r2 from eqn. 
4.77."

For fac:

"In some cases it can be useful to have different force constants for some 
restraints; this is controlled by the column fac. The force constant in the 
parameter file is multiplied by the value in the column fac for each restraint."


-Justin

--


Justin A. Lemkul, Ph.D.
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] distance restraints

[Banafsheh Mehrazma]

Dear all
I 'd like to do NOE distance restraints;  according to the chapter 4 of the
manual;
I should specify a section for [ distance_restraints] :

[ distance_restraints ]
; ai  aj  type  index  type’  low  up1  up2  fac
10   161010.00.30.41.0
10   281110.00.30.41.0
10   461110.00.30.41.0
16   221210.00.30.42.5
16   341310.00.50.61.0
.
althought I've studied the manual, it is still unclear to me, that how is
the index column defined? what are the numbers (0,1,2,3) implying? what
about the low, up1,up2, fac columns?

Thank you in advance
B.Mehrazma
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Re: [gmx-users] distance restraints fails

[Mark Abraham]

On 13/04/2012 3:08 AM, Qinghua Liao wrote:

Dear gmx users,

I tried to apply distance restraints to my system, but I found that it 
failed because the distance between the restraints atoms in the last 
frame is bigger than what we want.


Distance restraints aren't magic. There has to be an accessible 
simulation path from your initial conditions to one that satisfies the 
restraints. So far you haven't found one - there need not be one.


Mark


Here are the parameters for distance restraints in the topology file:

[ distance_restraints ]
; ai   aj type index type' low   up1   up2  fac
8  192  1   0   1   0.0   0.3   0.4   2.5
  18  203  1   0   1   0.0   0.3   0.4   2.5
  20  205  1   0   1   0.0   0.3   0.4   2.5

and also I tried this (added four other distance restraints in the 
same two groups):

[ distance_restraints ]
; ai   aj type index type' low   up1   up2  fac
   7  193  1   0   1   0.0   0.3   0.4   2.5
   8  192  1   0   1   0.0   0.3   0.4   2.5
  11  195  1   0   1   0.0   0.3   0.4   2.5
  18  202  1   0   1   0.0   0.3   0.4   2.5
  20  202  1   0   1   0.0   0.3   0.4   2.5
  18  203  1   0   1   0.0   0.3   0.4   2.5
  20  205  1   0   1   0.0   0.3   0.4   2.5

I am sure that the atom numbers are right.
And the following lines are the mdp file I used:

title   =  PDXN  of Abeta in H2O
;cpp =  /lib/cpp   ; prepocessor of the current machine
define  = ;-DPOSRES
integrator  =  md   ; molecular dynamics algorithm
tinit   =  0.0  ; start time and timestep in ps
dt  =  0.002; time step in ps
nsteps  =  100   ; number of steps for 1000 ns run
emtol   =  100; convergence criterion
emstep  =  0.05  ; intial step size
nstlist =  0   ; step frequency for updating neighbour 
list
ns_type =  simple ;grid ; method for neighbour 
searching (?)
nstxout =  5000 ; frequency for writing coords to 
output .trr file
nstvout =  0 ; frequency for writing velocities to 
output...should be same as nstxout

nstfout =  0; frequency for writing forces to output
nstlog  =  5000  ; frequency for writing energies to 
log file
nstenergy   =  5000  ; frequency for writing energies to 
energy file

nstxtcout   =  5000 ; frequency for writing coords to xtc traj
xtc_grps=  system   ; group(s) whose coords are to be 
written in xtc traj
energygrps  =  system   ; group(s) whose energy is to be 
written in energy file


;distance restraints
disre   = simple
disre_fc= 2 ; for the force, I tried 3000, 6000, 1 
and 15000, but all the tests failed

disre_mixed = yes
disre_weighting = equal
disre_tau   = 10
nstdisreout = 100
;
comm_mode   = angular
nstcomm = 10
comm_grps   = system
;
pbc =  no   ;xyz  ; use pbc
rlist   =  0 ;1.4  ; cutoff lengths (nm)
epsilon_r   =  1.0  ; Dielectric constant (DC) for 
twin-range or DC of reaction field

niter   =  100  ; Some thingies for future use
fourierspacing   =  0.16
fourier_nx  =  30
fourier_ny  =  30
fourier_nz  =  30
coulombtype =  Cut-off  ; truncation for minimisation, 
with large cutoff

rcoulomb=  0 ;1.4
rcoulomb-switch =  0
vdw-type = Cut-off  ; truncation for minimisation, 
with large cutoff

rvdw-switch  = 0
rvdw = 0 ; 1.4   ; cut-off lengths
;pme_order= 6; EWALD/PME/PPPM parameters
;ewald_rtol   = 1e-05
;ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = yes
 Free energy control stuff
free_energy  = yes
init_lambda  = 0.0
delta_lambda = 0
sc_alpha =0.5
sc-power =1.0
sc-sigma = 0.3
;nstcomm =  0; number of steps for centre of mass 
motion removal (in vacuo only!)

Tcoupl  =  V-rescale  ;Berendsen
tc_grps = system ;Other Water_and_ions
tau_t   = 0.5   ; 0.5
ref_t   = 300   ;   300
Pcoupl  =  no
;Pcoupltype  =  Isotropic
;tau_p   =  1.0  1.0 1.0
;ref_p   =  1.0  1.0 1.0
;compressibility =  4.5e-5   ; compressibility
annealing   =  no   ; SIMULATED ANNEALING CONTROL
;zero_temp_time  =  0; Time at which temperature should be 
zero (ps)

gen_vel =  yes
gen_temp=  300
gen_seed=  -1
constraints =  all-bonds  ; OPTIONS FOR BOND CONSTRAINTS
constraint-algorithm  = Lincs   ; Type of constraint algorithm
lincs_order =  4; Highest order in the expansion of 
the constraint coupling matrix
lincs_warnangle =

[gmx-users] distance restraints fails

[Qinghua Liao]

Dear gmx users,

I tried to apply distance restraints to my system, but I found that it
failed because the distance between the restraints atoms in the last frame
is bigger than what we want. Here are the parameters for distance
restraints in the topology file:

[ distance_restraints ]
; ai   aj type index type’ low   up1   up2  fac
8  192  1   0   1   0.0   0.3   0.4   2.5
  18  203  1   0   1   0.0   0.3   0.4   2.5
  20  205  1   0   1   0.0   0.3   0.4   2.5

and also I tried this (added four other distance restraints in the same two
groups):
[ distance_restraints ]
; ai   aj type index type’ low   up1   up2  fac
   7  193  1   0   1   0.0   0.3   0.4   2.5
   8  192  1   0   1   0.0   0.3   0.4   2.5
  11  195  1   0   1   0.0   0.3   0.4   2.5
  18  202  1   0   1   0.0   0.3   0.4   2.5
  20  202  1   0   1   0.0   0.3   0.4   2.5
  18  203  1   0   1   0.0   0.3   0.4   2.5
  20  205  1   0   1   0.0   0.3   0.4   2.5

I am sure that the atom numbers are right.
And the following lines are the mdp file I used:

title   =  PDXN  of Abeta in H2O
;cpp =  /lib/cpp   ; prepocessor of the current machine
define  = ;-DPOSRES
integrator  =  md   ; molecular dynamics algorithm
tinit   =  0.0  ; start time and timestep in ps
dt  =  0.002; time step in ps
nsteps  =  100   ; number of steps for 1000 ns run
emtol   =  100; convergence criterion
emstep  =  0.05  ; intial step size
nstlist =  0   ; step frequency for updating neighbour list
ns_type =  simple ;grid ; method for neighbour searching (?)
nstxout =  5000 ; frequency for writing coords to output
.trr file
nstvout =  0 ; frequency for writing velocities to
output...should be same as nstxout
nstfout =  0; frequency for writing forces to output
nstlog  =  5000  ; frequency for writing energies to log
file
nstenergy   =  5000  ; frequency for writing energies to energy
file
nstxtcout   =  5000 ; frequency for writing coords to xtc traj
xtc_grps=  system   ; group(s) whose coords are to be written
in xtc traj
energygrps  =  system   ; group(s) whose energy is to be written in
energy file

;distance restraints
disre   = simple
disre_fc= 2  ; for the force, I tried 3000, 6000, 1 and
15000, but all the tests failed
disre_mixed = yes
disre_weighting = equal
disre_tau   = 10
nstdisreout = 100
;
comm_mode   = angular
nstcomm = 10
comm_grps   = system
;
pbc =  no   ;xyz  ; use pbc
rlist   =  0 ;1.4  ; cutoff lengths (nm)
epsilon_r   =  1.0  ; Dielectric constant (DC) for twin-range
or DC of reaction field
niter   =  100  ; Some thingies for future use
fourierspacing=  0.16
fourier_nx  =  30
fourier_ny  =  30
fourier_nz  =  30
coulombtype =  Cut-off  ; truncation for minimisation, with
large cutoff
rcoulomb=  0 ;1.4
rcoulomb-switch =  0
vdw-type = Cut-off  ; truncation for minimisation, with
large cutoff
rvdw-switch  = 0
rvdw = 0 ; 1.4   ; cut-off lengths
;pme_order= 6; EWALD/PME/PPPM parameters
;ewald_rtol   = 1e-05
;ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = yes
 Free energy control stuff
free_energy  = yes
init_lambda  = 0.0
delta_lambda = 0
sc_alpha =0.5
sc-power =1.0
sc-sigma = 0.3
;nstcomm =  0; number of steps for centre of mass
motion removal (in vacuo only!)
Tcoupl  =  V-rescale  ;Berendsen
tc_grps = system ;Other Water_and_ions
tau_t   = 0.5   ; 0.5
ref_t   = 300   ;   300
Pcoupl  =  no
;Pcoupltype  =  Isotropic
;tau_p   =  1.0  1.0 1.0
;ref_p   =  1.0  1.0 1.0
;compressibility =  4.5e-5   ; compressibility
annealing   =  no   ; SIMULATED ANNEALING CONTROL
;zero_temp_time  =  0; Time at which temperature should be zero
(ps)
gen_vel =  yes
gen_temp=  300
gen_seed=  -1
constraints =  all-bonds  ; OPTIONS FOR BOND CONSTRAINTS
constraint-algorithm  = Lincs   ; Type of constraint algorithm
lincs_order =  4; Highest order in the expansion of the
constraint coupling matrix
lincs_warnangle =  30   ; Lincs will write a warning to the stderr
if in one step a bond rotates
; over more degrees than
unconstrained-start  = no   ; Do not constrain the start configuration
;Shake-SOR= no   ; Use successive overrelaxation to r

RE: [gmx-users] Distance Restraints on Protein - possible at all?

[NG HUI WEN]

Dear Mark,

Thanks for contributing your ideas and suggestions, really appreciate it.

The reason I am playing with distance restraints on my protein is because I am 
interested to see the effects of equilibrating a protein in membrane using the 
two different restraint methods i.e. distance vs. position.

Yes, without distance restraint (i.e. removing disre = simple in the mdp) will 
allow the simulation to run to completion very smoothly.

I will give Berendsen pressure coupling a shot and see how it goes. However, 
prior to applying distance restraint on my protein, I have ran 5ns of position 
restraint simulation (with P-R coupling) and there weren't any 
complaints/problems.

Many thanks again for your help.

Cheers,
Huiwen



From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Mark Abraham
Sent: Thursday, February 23, 2012 9:48 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Distance Restraints on Protein - possible at all?

On 22/02/2012 11:17 AM, NG HUI WEN wrote:


From: NG HUI WEN
Sent: Sunday, February 19, 2012 1:19 PM
To: gmx-users@gromacs.org<mailto:gmx-users@gromacs.org>
Subject: Distance Restraints on Protein - possible at all?


Dear gmxusers,



I have been trying to apply distance restraints on my protein but have been 
unsuccessful thus far.

For what purpose?





I have consulted the user forum previously and with some much-appreciated help 
I have managed to get my simulation (with distance restraints applied) to run. 
However, the joy did not last long as the simulation crashed very quickly 
(after ~40-50ps).

Do they run with no restraints?

P-R P-coupling is known to be unsuitable for equilibration (see manual), so 
that might be a factor here.

Mark
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Re: [gmx-users] Distance Restraints on Protein - possible at all?

[Mark Abraham]

On 22/02/2012 11:17 AM, NG HUI WEN wrote:


*From:*NG HUI WEN
*Sent:* Sunday, February 19, 2012 1:19 PM
*To:* gmx-users@gromacs.org
*Subject:* Distance Restraints on Protein - possible at all?

Dear gmxusers,

I have been trying to apply distance restraints on my protein but have 
been unsuccessful thus far.




For what purpose?

I have consulted the user forum previously and with some 
much-appreciated help I have managed to get my simulation (with 
distance restraints applied) to run. However, the joy did not last 
long as the simulation crashed very quickly (after ~40-50ps).




Do they run with no restraints?

P-R P-coupling is known to be unsuitable for equilibration (see manual), 
so that might be a factor here.


Mark

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[gmx-users] Distance Restraints on Protein - possible at all?

[NG HUI WEN]

From: NG HUI WEN
Sent: Sunday, February 19, 2012 1:19 PM
To: gmx-users@gromacs.org
Subject: Distance Restraints on Protein - possible at all?


Dear gmxusers,



I have been trying to apply distance restraints on my protein but have been 
unsuccessful thus far.



I have consulted the user forum previously and with some much-appreciated help 
I have managed to get my simulation (with distance restraints applied) to run. 
However, the joy did not last long as the simulation crashed very quickly 
(after ~40-50ps).



Below is an account of the attempts I made. Please bear with me as it is quite 
lenghty. I have tried to resolve the problem (but all to no avail) by :



a)changing the distance restraint group from CA to backbone - in case the 
protein is too floppy

b)fc from 1 to 1000 (default) to 0 - in order to check if the problem comes 
from the strenght of restraints



Below sum up what I had done:

1) prepare disre.itp file

genrestr -f posre_NVT_rep1.gro -o ca_disre.itp -disre



2) mdp looks:

title = NPT
define = -DDISRES

integrator = md
nsteps = 50
dt = 0.002

nstxout = 5
nstvout = 5
nstenergy = 2500
nstlog = 500

nstxtcout = 5
continuation = yes
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4

ns_type = grid
nstlist = 10
rlist = 1.2

rcoulomb = 1.2
rvdw = 1.2

coulombtype = PME
pme_order = 4
fourierspacing = 0.12
tcoupl = v-rescale
tc-grps = Protein POPC WATER_SOL_CL
tau_t = 0.1 0.1 0.1
ref_t = 310 310 310
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 1.0
ref_p = 1.0 1.0

compressibility = 4.5e-5 4.5e-5
pbc = xyz

DispCorr = EnerPres
gen_vel = no

nstcomm = 10
comm-mode = Linear
comm-grps = Protein_POPC WATER_SOL_CL
energygrps = Protein POPC WATER_SOL_CL
; DISRE parameters
disre = simple
disre-fc = (i)1/ (ii)1000 / (iii) 0



3) top file looks like this:

; Include forcefield parameters
#include "gromos53a6_lipid.ff/forcefield.itp"

;Include Protein Topology
#include "A2a.itp"

; Include Position restraint file
#ifdef DISRES
#include "ca_disre.itp"
#endif
;
#ifdef POSRES
#include "posre.itp"
#endif
;

;Include POPC topology
#include "popc.itp"
#ifdef LIPID_POSRES
#include "lipid_posre.itp"
#endif

;Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000

#endif



; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"



[ system ]

; Name
POPC and protein in water

[ molecules ]
; Compound #mols
Protein_chain_X 1
POPC 327
SOL 24767
CL 11



4) prepare .tpr file

grompp -f NPT_disres.mdp -c posre_NPT_rep1.gro -n index.ndx -p merged.top -t 
posre_NPT_rep1.cpt -o disre.tpr



5) mdrun

mdrun-mpi -v -s disre.tpr -deffnm disre -pd



The following are snippets of the output and log file before the simulations 
blew up:

i)fc= 1

step 21300, will finish Wed Feb 15 11:07:18 2012
step 21400, will finish Wed Feb 15 11:08:38 2012

Step 21481, time 42.962 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007728, max 0.339710 (between atoms 9 and 11)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length

Step 21482, time 42.964 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.022906, max 0.865028 (between atoms 12 and 16)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
16 17 31.6 0.1212 0.1447 0.1230
12 16 104.7 0.1266 0.0207 0.1530
9 11 110.7 0.0878 0.0397 0.1330
Wrote pdb files with previous and current coordinates

Step 21483, time 42.966 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009368, max 0.641094 (between atoms 9 and 11)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 33.3 0.0928 0.0961 0.1000
18 20 34.2 0.1474 0.1635 0.1470
16 18 60.0 0.1842 0.1310 0.1330
16 17 64.8 0.1447 0.1264 0.1230
14 15 30.4 0.0979 0.1525 0.1530
11 15 77.5 0.2435 0.1147 0.1470
11 12 34.5 0.2609 0.1633 0.1470
9 11 95.3 0.0397 0.2183 0.1330
Wrote pdb files with previous and current coordinates

Step 21484, time 42.968 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.013088, max 0.518530 (between atoms 12 and 16)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 40.0 0.0961 0.0952 0.1000
18 19 59.6 0.0996 0.0782 0.1000




ii) fc= 1000 (default)

step 21200, will finish Thu Feb 16 02:22:10 2012
step 21300, will finish Thu Feb 16 02:22:09 2012
step 21400, will finish Thu Feb 16 02:22:07 2012

Step 21481, time 42.962 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007728, max 0.339710 (between atoms 9 and 11)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length

Step 21482, time 42.964 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.022906, 

[gmx-users] distance restraints for atoms on 2 chains

[Sai Pooja]

Hi,

I have 5 chains in my Protein. I want to apply distance restraints for doing
Umbrella Sampling for 2 atoms on different chains. Is there a way to do this
since the two chains have separater itp files.

Pooja

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Re: [gmx-users] Distance Restraints: Inconsistent Shifts, LINCS Warnings, Number of grid cells is zero, XTC error

[Mark Abraham]

João M. Damas wrote:
What do you mean by mutually inconsistent? From what I understand, they 
aren't.


I mean a set for which there is no molecular arrangement that satisfies.

Also, [bonds] type 6 won't work for what I want, since I don't want to 
keep the molecules at a fixed distance but to prevent them from coming 
closer, i.e. I want a potential that depends on the distance between the 
atoms.


Testing the distance restraints can be quite exhaustive when you have 
about 160 restraints, and I am considering just the test case I'm 
trying, not the actual system which will have some more organic 
molecules, which will lead to a greater amount of combination of 
restraints...


#ifdef is your friend here...

[ distance_restraints ]



#ifdef BLAHBLAH



#endif

Now you just move the #ifdef to rearrange your test cases.

I might start with an even smaller test case until you prove you can 
deal with both the input formatting issues and the physics issues with 
it. Testing will be faster, for starters.


Mark

On Fri, Oct 9, 2009 at 12:51 AM, Mark Abraham > wrote:


João M. Damas wrote:

Gromacs users,

I have a small test system of about 2500 atoms which consists on
a few organic molecules in a box of water. I'm trying to use
distance restraints to keep each molecule apart from each other
and I've failed until now.

I'll start by saying that the simulation runs smoothly without
using distance restraints and that I've created a single
molecule topology that describes all organic molecules, allowing
the use of distance restraints. By applying just one distance
restraint between two atoms of different molecules, the
simulation still runs without problems. When I apply all the
distance restraints I want, the system crashes in the first few
steps with an XTC error, which is preceded by a few inconsistent
shifts and some LINCS warnings. Varying the number of restraints
that I use, makes the crash happen at later steps (500ish),
meanwhile giving a lot of inconsistent shifts before crashing
with a fatal error: Number of grid cells is zero. I know it
seems I'm experimenting blindly, but varying the number of
restraints was the first that occurred to me.
I've searched the list for similar problems and tried a few more
tests. I've turned off LINCS and reduced the time step and it
didn't solve the problem, the box blew up after a few steps due
to pressure problems. Since it could be a PBC problem, I tried
to increase the size of the box, but it didn't solve the
problem. Turning of PBC did solve the problem, but I really need
PBC. I've also changed the low, up1 and up2 to values inferior
to half the box size (I don't even care about the up1 and up2
values in this application, and I was setting them to 5.0 nm
before), but it didn't solve the problem either. I'm a little on
a dead end here and I was hoping anyone could give me some insight.

By the way, I'm using GROMACS 4.


The simplest explanation is that your sets of distance restraints
are mutually inconsistent. This destabilizes the system and
eventually leads to your symptoms. Consider using [bonds] type 6,
per advice of manual section 4.3.4. Either way, if you add these
restraints one by one after testing that the previous set seemed to
work OK (didn't crash, trajectory looks right), you may uncover your
issue.

Mark
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--
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613




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Re: [gmx-users] Distance Restraints: Inconsistent Shifts, LINCS Warnings, Number of grid cells is zero, XTC error

[João M . Damas]

What do you mean by mutually inconsistent? From what I understand, they
aren't.

Also, [bonds] type 6 won't work for what I want, since I don't want to keep
the molecules at a fixed distance but to prevent them from coming closer,
i.e. I want a potential that depends on the distance between the atoms.

Testing the distance restraints can be quite exhaustive when you have about
160 restraints, and I am considering just the test case I'm trying, not the
actual system which will have some more organic molecules, which will lead
to a greater amount of combination of restraints...

Thanks,
João

On Fri, Oct 9, 2009 at 12:51 AM, Mark Abraham wrote:

> João M. Damas wrote:
>
>> Gromacs users,
>>
>> I have a small test system of about 2500 atoms which consists on a few
>> organic molecules in a box of water. I'm trying to use distance restraints
>> to keep each molecule apart from each other and I've failed until now.
>>
>> I'll start by saying that the simulation runs smoothly without using
>> distance restraints and that I've created a single molecule topology that
>> describes all organic molecules, allowing the use of distance restraints. By
>> applying just one distance restraint between two atoms of different
>> molecules, the simulation still runs without problems. When I apply all the
>> distance restraints I want, the system crashes in the first few steps with
>> an XTC error, which is preceded by a few inconsistent shifts and some LINCS
>> warnings. Varying the number of restraints that I use, makes the crash
>> happen at later steps (500ish), meanwhile giving a lot of inconsistent
>> shifts before crashing with a fatal error: Number of grid cells is zero. I
>> know it seems I'm experimenting blindly, but varying the number of
>> restraints was the first that occurred to me.
>> I've searched the list for similar problems and tried a few more tests.
>> I've turned off LINCS and reduced the time step and it didn't solve the
>> problem, the box blew up after a few steps due to pressure problems. Since
>> it could be a PBC problem, I tried to increase the size of the box, but it
>> didn't solve the problem. Turning of PBC did solve the problem, but I really
>> need PBC. I've also changed the low, up1 and up2 to values inferior to half
>> the box size (I don't even care about the up1 and up2 values in this
>> application, and I was setting them to 5.0 nm before), but it didn't solve
>> the problem either. I'm a little on a dead end here and I was hoping anyone
>> could give me some insight.
>>
>> By the way, I'm using GROMACS 4.
>>
>
> The simplest explanation is that your sets of distance restraints are
> mutually inconsistent. This destabilizes the system and eventually leads to
> your symptoms. Consider using [bonds] type 6, per advice of manual section
> 4.3.4. Either way, if you add these restraints one by one after testing that
> the previous set seemed to work OK (didn't crash, trajectory looks right),
> you may uncover your issue.
>
> Mark
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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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Re: [gmx-users] Distance Restraints: Inconsistent Shifts, LINCS Warnings, Number of grid cells is zero, XTC error

[Mark Abraham]

João M. Damas wrote:

Gromacs users,

I have a small test system of about 2500 atoms which consists on a few 
organic molecules in a box of water. I'm trying to use distance 
restraints to keep each molecule apart from each other and I've failed 
until now.


I'll start by saying that the simulation runs smoothly without using 
distance restraints and that I've created a single molecule topology 
that describes all organic molecules, allowing the use of distance 
restraints. By applying just one distance restraint between two atoms of 
different molecules, the simulation still runs without problems. When I 
apply all the distance restraints I want, the system crashes in the 
first few steps with an XTC error, which is preceded by a few 
inconsistent shifts and some LINCS warnings. Varying the number of 
restraints that I use, makes the crash happen at later steps (500ish), 
meanwhile giving a lot of inconsistent shifts before crashing with a 
fatal error: Number of grid cells is zero. I know it seems I'm 
experimenting blindly, but varying the number of restraints was the 
first that occurred to me.
I've searched the list for similar problems and tried a few more tests. 
I've turned off LINCS and reduced the time step and it didn't solve the 
problem, the box blew up after a few steps due to pressure problems. 
Since it could be a PBC problem, I tried to increase the size of the 
box, but it didn't solve the problem. Turning of PBC did solve the 
problem, but I really need PBC. I've also changed the low, up1 and up2 
to values inferior to half the box size (I don't even care about the up1 
and up2 values in this application, and I was setting them to 5.0 nm 
before), but it didn't solve the problem either. I'm a little on a dead 
end here and I was hoping anyone could give me some insight.


By the way, I'm using GROMACS 4.


The simplest explanation is that your sets of distance restraints are 
mutually inconsistent. This destabilizes the system and eventually leads 
to your symptoms. Consider using [bonds] type 6, per advice of manual 
section 4.3.4. Either way, if you add these restraints one by one after 
testing that the previous set seemed to work OK (didn't crash, 
trajectory looks right), you may uncover your issue.


Mark
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[gmx-users] Distance Restraints: Inconsistent Shifts, LINCS Warnings, Number of grid cells is zero, XTC error

[João M . Damas]

Gromacs users,
I have a small test system of about 2500 atoms which consists on a few
organic molecules in a box of water. I'm trying to use distance restraints
to keep each molecule apart from each other and I've failed until now.

I'll start by saying that the simulation runs smoothly without using
distance restraints and that I've created a single molecule topology that
describes all organic molecules, allowing the use of distance restraints. By
applying just one distance restraint between two atoms of different
molecules, the simulation still runs without problems. When I apply all the
distance restraints I want, the system crashes in the first few steps with
an XTC error, which is preceded by a few inconsistent shifts and some LINCS
warnings. Varying the number of restraints that I use, makes the crash
happen at later steps (500ish), meanwhile giving a lot of inconsistent
shifts before crashing with a fatal error: Number of grid cells is zero. I
know it seems I'm experimenting blindly, but varying the number of
restraints was the first that occurred to me.
 I've searched the list for similar problems and tried a few more tests.
I've turned off LINCS and reduced the time step and it didn't solve the
problem, the box blew up after a few steps due to pressure problems. Since
it could be a PBC problem, I tried to increase the size of the box, but it
didn't solve the problem. Turning of PBC did solve the problem, but I really
need PBC. I've also changed the low, up1 and up2 to values inferior to half
the box size (I don't even care about the up1 and up2 values in this
application, and I was setting them to 5.0 nm before), but it didn't solve
the problem either. I'm a little on a dead end here and I was hoping anyone
could give me some insight.

By the way, I'm using GROMACS 4.

Thanks in advance and sorry if I sounded confusing.

Best regards,
João
-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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[gmx-users] distance restraints in Gromacs 4.0.4

[Ivan Gladich]

Dear users
I have found a problem for the  distance constraint in the version
4.0.4 of gromacs.
I am trying to simulate a water droplet around an ion. To do that I use
a distance restraint armonic potential (pag.66, manual version 4).
During my simulation the shape of my sphere fluctuating too much and
many molecules leave the sphere even if the restoring force is big (I
use for restraint armonic potential a constant k=1e4 KJ mol^-1 nm^-2 ).
The problem disappear if I run the exactly same simulation with gromacs
3.3.3.:the spherical shape is always conserve and no molecules leave the
sphere.

Furthermore, if I am trying to run droplet larger than 1.0 nm radius
(e.g. 1.6 nm). These  simulation at a certain point stop, giving me the
following error

** glibc detected *** Dmdrun: munmap_chunk(): invalid pointer:
0x00a72bd0 ***

The same simulation in the version 3.3.3 runs without any problem.

Do you know what kind of problem could be?
Has the version 4.0.4  some problems with distance restrains?

Thank you in advance for any help or suggestion
 Ivan Gladich
-- 
---
Ivan Gladich

Dreyfus Postdoctoral Fellow
Department of Chemistry
Purdue University
560 Oval Drive, box 140
West Lafayette
IN 47906 USA

Room: 265C
Tel:765-494-5225
e-mail: iglad...@purdue.edu
web page: http://web.ics.purdue.edu/~igladich/



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[gmx-users] distance restraints for alpha helix

[abhigna polavarapu]

Dear all,
 I am trying to rebuild the alpha helix of one the chains
which got destroyed during the simulation. I found that we can do that
by distance restraints. So my question what is a better way of
distance restraints i.e should I restrain the hydrogen bonds of the
helix or any particular bond distances. I was not clear when I read
the chapter 4 in manual, what type' should I use for this, are these
parameterized anywhere because the manual says type' should be 1 for
bonds but for hydrogen bonds it varies from 0-2. I found an exercise
by David van der Spoel
http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2004/exercises/index_html
but could not access the files, so I was not clear what atoms did he
use for restraints.

Thank you
abhigna
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RE: [gmx-users] distance restraints and domain decomposition

[Berk Hess]

Hi,

Is this the only output you got?
There is no error message at all?

If there was no error message and you get the error quickly
(i.e. not after hours of simulations),
please file a bugzilla entry, give the exact command line
of mpirun and mdrun and attach your tpr file.

Berk

> Date: Fri, 5 Dec 2008 14:33:30 -0500
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] distance restraints and domain decomposition
> 
> Hi All,
> 
> I am trying to run a simulation on a 13 residue peptide fragment with
> distance restraints in parallel and I'm getting a fatal error when I try
> to implement mdrun. Here is my nohup.out file:
> 
>  :-)  G  R  O  M  A  C  S  (-:
> 
>Giving Russians Opium May Alter Current Situation
> 
>  :-)  VERSION 4.0  (-:
> 
> 
>   Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>  Copyright (c) 2001-2008, The GROMACS development team,
> check out http://www.gromacs.org for more information.
> 
>  This program is free software; you can redistribute it and/or
>   modify it under the terms of the GNU General Public License
>  as published by the Free Software Foundation; either version 2
>  of the License, or (at your option) any later version.
> 
>:-)  mdrunmpi  (-:
> 
> Option Filename  Type Description
> 
>   -s md.tpr  InputRun input file: tpr tpb tpa
>   -o md.trr  Output   Full precision trajectory: trr trj cpt
>   -x md.xtc  Output, Opt! Compressed trajectory (portable xdr format)
> -cpi  state.cpt  Input, Opt.  Checkpoint file
> -cpo  state.cpt  Output, Opt. Checkpoint file
>   -c md.gro  Output   Structure file: gro g96 pdb
>   -e md.edr  Output   Energy file: edr ene
>   -g md.log  Output   Log file
> -dgdl  dgdl.xvg  Output, Opt. xvgr/xmgr file
> -fieldfield.xvg  Output, Opt. xvgr/xmgr file
> -tabletable.xvg  Input, Opt.  xvgr/xmgr file
> -tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
> -tableb   table.xvg  Input, Opt.  xvgr/xmgr file
> -rerunrerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
> -tpitpi.xvg  Output, Opt. xvgr/xmgr file
> -tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
>  -eisam.edi  Input, Opt.  ED sampling input
>  -eosam.edo  Output, Opt. ED sampling output
>   -j   wham.gct  Input, Opt.  General coupling stuff
>  -jobam.gct  Output, Opt. General coupling stuff
> -ffout  gct.xvg  Output, Opt. xvgr/xmgr file
> -devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
> -runav  runaver.xvg  Output, Opt. xvgr/xmgr file
>  -px  pullx.xvg  Output, Opt. xvgr/xmgr file
>  -pf  pullf.xvg  Output, Opt. xvgr/xmgr file
> -mtx nm.mtx  Output, Opt. Hessian matrix
>  -dn dipole.ndx  Output, Opt. Index file
> 
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -niceint0   Set the nicelevel
> -deffnm  string Set the default filename for all file options
> -[no]xvgrbool   yes Add specific codes (legends etc.) in the output
> xvg files for the xmgrace program
> -[no]pd  bool   no  Use particle decompostion
> -dd  vector 0 0 0   Domain decomposition grid, 0 is optimize
> -npmeint-1  Number of separate nodes to be used for PME, -1
> is guess
> -ddorder enum   interleave  DD node order: interleave, pp_pme or
> cartesian
> -[no]ddcheck bool   yes Check for all bonded interactions with DD
> -rdd real   0   The maximum distance for bonded interactions with
> DD (nm), 0 is determine from initial coordinates
> -rconreal   0   Maximum distance for P-LINCS (nm), 0 is estimate
> -dlb enum   autoDynamic load balancing (with DD): auto, no or yes
> -dds real   0.8 Minimum allowed dlb scaling of the DD cell size
> -[no]sum bool   yes Sum the energies at every step
> -[no]v   bool   no  Be loud and noisy
> -[no]compact bool   yes Write a compact log file
> -[no]seppot  bool   no  Write separate V and dVdl terms for each
> interaction type and node to the log file(s)
> -pforce  real   -1  Print all forces larger than this (kJ/mol nm)

[gmx-users] distance restraints and domain decomposition

[map110+]

Hi All,

I am trying to run a simulation on a 13 residue peptide fragment with
distance restraints in parallel and I'm getting a fatal error when I try
to implement mdrun. Here is my nohup.out file:

 :-)  G  R  O  M  A  C  S  (-:

   Giving Russians Opium May Alter Current Situation

 :-)  VERSION 4.0  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

   :-)  mdrunmpi  (-:

Option Filename  Type Description

  -s md.tpr  InputRun input file: tpr tpb tpa
  -o md.trr  Output   Full precision trajectory: trr trj cpt
  -x md.xtc  Output, Opt! Compressed trajectory (portable xdr format)
-cpi  state.cpt  Input, Opt.  Checkpoint file
-cpo  state.cpt  Output, Opt. Checkpoint file
  -c md.gro  Output   Structure file: gro g96 pdb
  -e md.edr  Output   Energy file: edr ene
  -g md.log  Output   Log file
-dgdl  dgdl.xvg  Output, Opt. xvgr/xmgr file
-fieldfield.xvg  Output, Opt. xvgr/xmgr file
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
-tableb   table.xvg  Input, Opt.  xvgr/xmgr file
-rerunrerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpitpi.xvg  Output, Opt. xvgr/xmgr file
-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
 -eisam.edi  Input, Opt.  ED sampling input
 -eosam.edo  Output, Opt. ED sampling output
  -j   wham.gct  Input, Opt.  General coupling stuff
 -jobam.gct  Output, Opt. General coupling stuff
-ffout  gct.xvg  Output, Opt. xvgr/xmgr file
-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
-runav  runaver.xvg  Output, Opt. xvgr/xmgr file
 -px  pullx.xvg  Output, Opt. xvgr/xmgr file
 -pf  pullf.xvg  Output, Opt. xvgr/xmgr file
-mtx nm.mtx  Output, Opt. Hessian matrix
 -dn dipole.ndx  Output, Opt. Index file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint0   Set the nicelevel
-deffnm  string Set the default filename for all file options
-[no]xvgrbool   yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-[no]pd  bool   no  Use particle decompostion
-dd  vector 0 0 0   Domain decomposition grid, 0 is optimize
-npmeint-1  Number of separate nodes to be used for PME, -1
is guess
-ddorder enum   interleave  DD node order: interleave, pp_pme or
cartesian
-[no]ddcheck bool   yes Check for all bonded interactions with DD
-rdd real   0   The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rconreal   0   Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum   autoDynamic load balancing (with DD): auto, no or yes
-dds real   0.8 Minimum allowed dlb scaling of the DD cell size
-[no]sum bool   yes Sum the energies at every step
-[no]v   bool   no  Be loud and noisy
-[no]compact bool   yes Write a compact log file
-[no]seppot  bool   no  Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce  real   -1  Print all forces larger than this (kJ/mol nm)
-[no]reprod  bool   no  Try to avoid optimizations that affect binary
reproducibility
-cpt real   15  Checkpoint interval (minutes)
-[no]append  bool   no  Append to previous output files when restarting
from checkpoint
-maxhreal   -1  Terminate after 0.99 times this time (hours)
-multi   int0   Do multiple simulations in parallel
-replex  int0   Attempt replica exchange every # steps
-reseed  int-1  Seed for replica exchange, -1 is generate a seed
-[no]glasbool   no  Do glass simulation with special long range
corrections
-[no]ionize  bool   no  Do a simulation including the effect of an X-Ray
bombardment on your system


Back Off! I just backed up md.log to ./#md.log.1#
Reading file md.tpr, VE

[gmx-users] Distance Restraints Violations

[Francisco Gomes Neto]

Hi, all:

Im using g_disre in gmx3.3.1 to calculate violations of distance
 restraints  in a simulation and I saw the message:

 Fatal error:
 tpr inconsistency. ndr = 0, label = 1

 The gmxdump of tpr shows

  functype[459]=DISRES, label=   1, type=1, low= 1.8007e-01, up1=
 2.8001e-01, up2= 3.3013e-01, fac= 1.e+00)


 Im looking for hints in the gmx-users mail box and ...

 "Usually problems here are related to the topology. Check whether one of
 the restraints is missing (typically the one with label = 362). This
 check is in g_disre only, not in mdrun or grompp. Maybe it should be in
 the latter..."

 It seems that the restraint is there Am I forgeting something?


 Any hint will be sincerely appreciated!
 Im lost here!

 Francisco
-- 

Francisco Gomes Neto
Centro Nacional de Ressonancia Magnetica Nuclear - CNRMN
Av. Brigadeiro Trompowisky, s/n - Predio CCS - Sala E-10
Rio de Janeiro - RJ - CEP 21.941-590
e-mail: [EMAIL PROTECTED]
http://cnrmn.bioqmed.ufrj.br


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Re: [gmx-users] distance restraints for a pdb file?

[David van der Spoel]

Robert Selwyne wrote:

Dear All
Is there any way of generating the distance restraints for a pdb file? Do
any of the gromacs command support this problem or it has to be filled out
manually?
Best wishes
Robert


what do you mean generating the distance restraints? from nMR data? in 
that case there is a script in src/contrib/scripts


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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] distance restraints for a pdb file?

[Robert Selwyne]

Dear All
Is there any way of generating the distance restraints for a pdb file? Do
any of the gromacs command support this problem or it has to be filled out
manually?
Best wishes
Robert

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Re: [gmx-users] Distance restraints

[Mark Abraham]

zhong qiang wrote:
> Hi:
>   I want to constuct my .top file, In my molecular system four calcium 
> ions binding at four site, I use pdb2gmx  make a top file, But there is 
> not topology information about calcium ions, I insert a distance 
> restraints in .top file, just like below:
> [ distance restraints ]
> ;  aiaj  type index type’ low up1 up2 fac
> 1460   207 1 2   1   0.0 0.3 0.4 1.0
> 1460   208 1 2   1   0.0 0.3 0.4 1.0
> 1460   210 1 2   1   0.0 0.3 0.4 1.0
> 1460   229 1 2   1   0.0 0.3 0.4 1.0
> .
> 
> then I run
> grompp -f fullmd_sol.mdp -c minimized_water.gro -p 1ckk.top -o fullmd.tpr
> But error message present:
> ERROR 1 [file "1ckk.top", line 9029]:
>  Invalid directive distance restraints
> 
> Then I delete line [ distance restraints ]

!! That's a bit like a car mechanic telling you your car won't start
because your battery is flat, and so you take it out and try again!

> the error report:
> Fatal error:
> Incorrect number of parameters - found 4, expected 3 or 6.
> 
> Could somebody tell me how to add a distance restraints correctly?

Yep. The first step will be to spell it like it is in the manual...
"distance_restraints"

Mark
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[gmx-users] Distance restraints

[zhong qiang]

Hi:
  I want to constuct my .top file, In my molecular system four calcium 
ions binding at four site, I use pdb2gmx  make a top file, But there is not 
topology information about calcium ions, I insert a distance restraints in 
.top file, just like below:

[ distance restraints ]
;  aiaj  type index type’ low up1 up2 fac
1460   207 1 2   1   0.0 0.3 0.4 1.0
1460   208 1 2   1   0.0 0.3 0.4 1.0
1460   210 1 2   1   0.0 0.3 0.4 1.0
1460   229 1 2   1   0.0 0.3 0.4 1.0
.

then I run
grompp -f fullmd_sol.mdp -c minimized_water.gro -p 1ckk.top -o fullmd.tpr
But error message present:
ERROR 1 [file "1ckk.top", line 9029]:
 Invalid directive distance restraints

Then I delete line [ distance restraints ]
the error report:
Fatal error:
Incorrect number of parameters - found 4, expected 3 or 6.

Could somebody tell me how to add a distance restraints correctly?
Thank you very much!

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RE: [gmx-users] distance restraints: -merge

[Berk Hess]

From: "Owen, Michael" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: 
Subject: [gmx-users] distance restraints: -merge
Date: Tue, 26 Sep 2006 11:10:15 -0500


Fellow gmx-users,

I would like to constrain the distance of an ion to specific atoms of a 
protein.  I recently read a message in which the use of the option -merge 
in the pdb2gmx program was suggested.  How can I use this option to form 
these constraints?


The -merge option is useful for merge two molecules.

I assume that in your case the ion consists of just one atom.
Then it is easier to just add this one atom by hand at the end of atoms
of your protein and add the distance restraint.

Berk.


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[gmx-users] distance restraints: -merge

[Owen, Michael]

Title: distance restraints: -merge







Fellow gmx-users,

I would like to constrain the distance of an ion to specific atoms of a protein.  I recently read a message in which the use of the option -merge in the pdb2gmx program was suggested.  How can I use this option to form these constraints?

Thank you for your assistance,

Michael Owen



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Re: [gmx-users] Distance restraints

[David Mobley]

If I remember correctly, distance restraints (for some reason) only
work between multiple atoms of the same "molecule". By molecule, I
don't mean that they have to be joined by bonds; rather, both need to
appear in the same [ moleculetype ] section of the topology, which
means that GROMACS considers them a "molecule".

The other way of thinking of this is that distance restraints use the
atom numbers from the [ atoms ] section that they follow. If you're
trying to use the atom numbers from your gro file, it won't work;
GROMACS won't understand them. So in your case, it means you need to
get the parameters for your ions out of your ions.itp file and insert
explicit ions with atom numbers into the appropriate sections of your
topology, following the peptide atoms, probably.

I hope that makes sense. Search the mailing list on distance
restraints if you need more; this has been discussed on thel ist
before.

David

On 8/3/06, Owen, Michael <[EMAIL PROTECTED]> wrote:





Hello,

 I am trying to use NMR restraints to position a Cu2+ ion around specific
residues of a peptide.  I added Cu2+ using "genion" and then initiated
"grompp" before an energy minim minimization.  I received the following
error message while executing "grompp":


 ---
 Program grompp, VERSION 3.3.1
 Source code file: toppush.c, line: 1108

 Fatal error:
 [ file "Ab_Cu.top", line 5864 ]:
  Atom index (67248) in distance_restraints out of bounds (1-1)
 ---


 Below is the entry in the topology file.  Line 5864 contains the value 97
and the value 67248 refers is the atom number of the Cu2+ ion.


 [ distance_restraints ]

 ;ai aj  typeindex   type'   low up1 up2 fac
 67248   97  1   1   1   0.185   0.195   0.2 1.0
 67248   196 1   1   1   0.185   0.195   0.2 1.0
 67248   213 1   1   1   0.185   0.195   0.2 1.0
 67248   148 1   1   1   0.195   0.205   0.211.0

 Could you suggest any changes that would eliminate my error?

 Thanks in advance,

 Michael Owen
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[gmx-users] Distance restraints

[Owen, Michael]

Title: Distance restraints







Hello,

I am trying to use NMR restraints to position a Cu2+ ion around specific residues of a peptide.  I added Cu2+ using "genion" and then initiated "grompp" before an energy minim minimization.  I received the following error message while executing "grompp":


---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 1108

Fatal error:
[ file "Ab_Cu.top", line 5864 ]:
 Atom index (67248) in distance_restraints out of bounds (1-1)
---


Below is the entry in the topology file.  Line 5864 contains the value 97 and the value 67248 refers is the atom number of the Cu2+ ion.


[ distance_restraints ]

;ai aj  type    index   type'   low up1 up2 fac
67248   97  1   1   1   0.185   0.195   0.2 1.0
67248   196 1   1   1   0.185   0.195   0.2 1.0
67248   213 1   1   1   0.185   0.195   0.2 1.0
67248   148 1   1   1   0.195   0.205   0.21    1.0

Could you suggest any changes that would eliminate my error?

Thanks in advance,

Michael Owen



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Re: [gmx-users] distance restraints problem

[Mark Abraham]

Michal Kolinski wrote:

Dear All
 
I’m using distance restraints to force proper orientation of the  ligand 
in the active site of  the receptor protein (I’m investigating different 
binding modes).

I encountered a strange problem when defining distance restraints.
I have protein and ligand topology combined in one itp file.
At the end of this topology file (itp) I defined atoms pairs for 
distance restraints:

….
[ distance_restraints ]
; aiaj   type index  typelow   up1up2fac
  1384  40361 0 1   0.0  0.15   0.25   2.0
  2957  40461 1 1   0.0  0.15   0.25   2.0
  2957  40571 1 1   0.0  0.15   0.25   2.0
 
When looking at trajectory file I noticed that restraints are present 
but not between defined atoms but probably between pairs:
 
1383 4035

2956 4045
2956 4056


How did you tell this? If using gmxdump, then see below.

I checked the tpr file: gmxdump_mpi3  -s posre100.tpr and I found that 
position restraints are not between defined pairs but rather 
between (atom-1,atom-1).

…
Dis. Rest.:
nr: 9
multinr[division over processors]: 9 9 9 9 9 9 9 9 9 9 9 9 …
iatoms:
   0 type=1244 (DISRES) 1383 4035
   1 type=1245 (DISRES) 2956 4045
   2 type=1245 (DISRES) 2956 4056


Array numbering in C starts with zero. PDB atom numbering starts with 
one. pdb2gmx is just dumping the contents of arrays, without regard to 
whether they correspond to atoms or not. Doing anything else would be 
bizarre with respect to the conventions of C and programming in general.


Mark
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Re: [gmx-users] distance restraints problem

[Jim Fonseca]

I believe that there's no problem with the numbering.  The numbering in the topology will start with 1, however due to Gromacs' implementation, the indexing starts at 0. So, atom 4036 in your .itp corresponds to 4035 in the trajectory file.  Note that if you look in your trajectory file you should see an atom indexed at 0. For example:      x[    0]={ 9.82700e+00,  6.47400e+00,  1.01800e+01}hthJimOn Mar 3, 2006, at 10:00 AM, Michal Kolinski wrote: Dear All   I’m using distance restraints to force proper orientation of the  ligand in the active site of  the receptor protein (I’m investigating different binding modes).I encountered a strange problem when defining distance restraints.I have protein and ligand topology combined in one itp file.At the end of this topology file (itp) I defined atoms pairs for distance restraints:….[ distance_restraints ]; ai    aj   type index  type    low   up1    up2    fac  1384  4036    1 0 1   0.0  0.15   0.25   2.0  2957  4046    1 1 1   0.0  0.15   0.25   2.0  2957  4057    1 1 1   0.0  0.15   0.25   2.0   When looking at trajectory file I noticed that restraints are present but not between defined atoms but probably between pairs:   1383 40352956 40452956 4056   I checked the tpr file: gmxdump_mpi3  -s posre100.tpr and I found that position restraints are not between defined pairs but rather between (atom-1,atom-1).…Dis. Rest.:    nr: 9    multinr[division over processors]: 9 9 9 9 9 9 9 9 9 9 9 9 …    iatoms:   0 type=1244 (DISRES) 1383 4035   1 type=1245 (DISRES) 2956 4045   2 type=1245 (DISRES) 2956 4056…   Numbering of atoms in my topology file is correct so I guess it’s not the case.  What might be the problem.  Am I doing something wrong.  I’m using gromacs3.3. Please give me comment on this and thank you for help.   Best regardsMichal___gmx-users mailing list    gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___
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[gmx-users] distance restraints problem

[Michal Kolinski]

Dear All
 
I’m using distance restraints to force proper 
orientation of the  ligand in the active site of  the receptor protein 
(I’m investigating different binding modes).I encountered a strange problem 
when defining distance restraints.I have protein and ligand topology 
combined in one itp file.At the end of this topology file (itp) I defined 
atoms pairs for distance restraints:….[ distance_restraints ]; 
ai    aj   type 
index  type    low   
up1    up2    fac  1384  
4036    1 
0 
1   0.0  0.15   
0.25   2.0  2957  4046    
1 
1 
1   0.0  0.15   
0.25   2.0  2957  4057    
1 
1 
1   0.0  0.15   
0.25   2.0
 
When looking at trajectory file I noticed that 
restraints are present but not between defined atoms but probably between 
pairs:
 
1383 40352956 40452956 4056
 
I checked the tpr file: gmxdump_mpi3  -s 
posre100.tpr and I found that position restraints are not between defined pairs 
but rather between 
(atom-1,atom-1).…Dis. 
Rest.:    nr: 
9    
multinr[division over processors]: 9 9 9 9 9 9 9 9 9 9 9 9 
…    
iatoms:   
0 type=1244 (DISRES) 1383 
4035   
1 type=1245 (DISRES) 2956 
4045   
2 type=1245 (DISRES) 2956 4056…
 
Numbering of atoms in my topology file is correct 
so I guess it’s not the case.  What might be the problem.  Am I doing 
something wrong.  I’m using gromacs3.3. Please give me comment on this 
and thank you for help.
 
Best 
regardsMichal
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