Re: [gmx-users] Energy Minimization Error

[Amali Guruge]

Dear Gromacs users,

When I tried to run the equilibration run, it gave several LINCS WARNINGS.
However, that equilibration run is completed by the Gromacs. Do I have to
concern about these warnings or can I ignore those?

Thank you.

Sincerely,
A. Guruge

On Fri, Oct 20, 2017 at 11:22 AM, Justin Lemkul  wrote:

>
>
> On 10/19/17 8:21 PM, Amali Guruge wrote:
>
>> Dear Gromacs users,
>>
>> Thank you very much for the reply. My concern is "step 11: One or more
>> water molecules can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate". What
>> should I do to avoid it?
>>
>
> That happens often during minimization, especially the early steps. If it
> doesn't come back up again, it's fine. It should never happen during MD.
>
> -Justin
>
>
> Thank you.
>>
>> On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul  wrote:
>>
>>
>>> On 10/19/17 8:10 PM, Amali Guruge wrote:
>>>
>>> Dear Gromacs Users,

 I tried to energy minimize my system using the steep integrator.
 However,
 it gave the following message.

 Steepest Descents:
  Tolerance (Fmax)   =  5.0e+02
  Number of steps= 2000
 Step=0, Dmax= 1.0e-02 nm, Epot=  3.96157e+06 Fmax= 1.00697e+06,
 atom=
 14611
 Step=1, Dmax= 1.0e-02 nm, Epot=  2.99970e+06 Fmax= 4.04778e+05,
 atom=
 18527
 Step=2, Dmax= 1.2e-02 nm, Epot=  1.54766e+06 Fmax= 1.52387e+05,
 atom=
 1005
 Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04,
 atom=
 6994
 Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04,
 atom=
 58902
 Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04,
 atom=
 515
 Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04,
 atom=
 188631
 Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04,
 atom=
 188631
 Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04,
 atom=
 188631
 Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04,
 atom=
 188631
 Step=   10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04,
 atom=
 188631

 step 11: One or more water molecules can not be settled.
 Check for bad contacts and/or reduce the timestep if appropriate.

 After 2000 steps it says,

 Steepest Descents did not converge to Fmax < 500 in 2001 steps.
 Potential Energy  = -4.6310655e+06
 Maximum force =  6.7453154e+03 on atom 18769
 Norm of force =  3.3632809e+01

 Simulation ended prematurely, no performance report will be written.


 my em.mdp file contains following parameters.

 integrator=  steep; simulation algorithm
 dt=  0.002; time step (ps)
 nsteps=  2000; # steps
 comm_mode=  linear; c.o.m. motion reset
 ;
 ;Energy Minimization
 emtol=  500; converged F lt value (kJ mol-1
 nm-1)
 emstep=  0.01 ; initial step size (nm)
 ;
 ;Output Control
 nstxout=  5 ; write coordinates to .trr
 nstvout=  5; write velocities to .trr
 nstlog=  5; write energies to .log
 nstenergy=  1; write energies to .edr
 ;
 ;Neightbour Searching
 cutoff-scheme   =  Verlet; scheme used for
 generating pair list
 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)
 ;
 ;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
 ;
 ;Temperature Coupling
 Tcoupl=  no; type of temperature coupling
 ;
 ;Pressure Coupling
 Pcoupl=  no ; type of pressure coupling
 ;
 ;Velocity Generation
 gen_vel=  no ; generate initial velocities
 ;
 ;Bonds
 constraints=  none; bond constraint type

 I used gmx solvate to add water 

Re: [gmx-users] Energy Minimization Error

[Justin Lemkul]

On 10/19/17 8:21 PM, Amali Guruge wrote:

Dear Gromacs users,

Thank you very much for the reply. My concern is "step 11: One or more
water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate". What
should I do to avoid it?


That happens often during minimization, especially the early steps. If 
it doesn't come back up again, it's fine. It should never happen during MD.


-Justin


Thank you.

On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul  wrote:



On 10/19/17 8:10 PM, Amali Guruge wrote:


Dear Gromacs Users,

I tried to energy minimize my system using the steep integrator. However,
it gave the following message.

Steepest Descents:
 Tolerance (Fmax)   =  5.0e+02
 Number of steps= 2000
Step=0, Dmax= 1.0e-02 nm, Epot=  3.96157e+06 Fmax= 1.00697e+06, atom=
14611
Step=1, Dmax= 1.0e-02 nm, Epot=  2.99970e+06 Fmax= 4.04778e+05, atom=
18527
Step=2, Dmax= 1.2e-02 nm, Epot=  1.54766e+06 Fmax= 1.52387e+05, atom=
1005
Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom=
6994
Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom=
58902
Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom=
515
Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom=
188631
Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom=
188631
Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom=
188631
Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom=
188631
Step=   10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom=
188631

step 11: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

After 2000 steps it says,

Steepest Descents did not converge to Fmax < 500 in 2001 steps.
Potential Energy  = -4.6310655e+06
Maximum force =  6.7453154e+03 on atom 18769
Norm of force =  3.3632809e+01

Simulation ended prematurely, no performance report will be written.


my em.mdp file contains following parameters.

integrator=  steep; simulation algorithm
dt=  0.002; time step (ps)
nsteps=  2000; # steps
comm_mode=  linear; c.o.m. motion reset
;
;Energy Minimization
emtol=  500; converged F lt value (kJ mol-1 nm-1)
emstep=  0.01 ; initial step size (nm)
;
;Output Control
nstxout=  5 ; write coordinates to .trr
nstvout=  5; write velocities to .trr
nstlog=  5; write energies to .log
nstenergy=  1; write energies to .edr
;
;Neightbour Searching
cutoff-scheme   =  Verlet; scheme used for
generating pair list
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)
;
;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
;
;Temperature Coupling
Tcoupl=  no; type of temperature coupling
;
;Pressure Coupling
Pcoupl=  no ; type of pressure coupling
;
;Velocity Generation
gen_vel=  no ; generate initial velocities
;
;Bonds
constraints=  none; bond constraint type

I used gmx solvate to add water molecules to the system.

How could I get rid of bad contacts of water molecules? Appreciate if
anyone help me to solve the problem.


mdrun stopped after 2000 steps because you told it to. You need to
minimize further, so increase nsteps (or set it to -1 to let mdrun go as
long as it needs to without having to guess a number).

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Energy Minimization Error

[Amali Guruge]

Dear Gromacs users,

Thank you very much for the reply. My concern is "step 11: One or more
water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate". What
should I do to avoid it?

Thank you.

On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul  wrote:

>
>
> On 10/19/17 8:10 PM, Amali Guruge wrote:
>
>> Dear Gromacs Users,
>>
>> I tried to energy minimize my system using the steep integrator. However,
>> it gave the following message.
>>
>> Steepest Descents:
>> Tolerance (Fmax)   =  5.0e+02
>> Number of steps= 2000
>> Step=0, Dmax= 1.0e-02 nm, Epot=  3.96157e+06 Fmax= 1.00697e+06, atom=
>> 14611
>> Step=1, Dmax= 1.0e-02 nm, Epot=  2.99970e+06 Fmax= 4.04778e+05, atom=
>> 18527
>> Step=2, Dmax= 1.2e-02 nm, Epot=  1.54766e+06 Fmax= 1.52387e+05, atom=
>> 1005
>> Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom=
>> 6994
>> Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom=
>> 58902
>> Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom=
>> 515
>> Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom=
>> 188631
>> Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom=
>> 188631
>> Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom=
>> 188631
>> Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom=
>> 188631
>> Step=   10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom=
>> 188631
>>
>> step 11: One or more water molecules can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>>
>> After 2000 steps it says,
>>
>> Steepest Descents did not converge to Fmax < 500 in 2001 steps.
>> Potential Energy  = -4.6310655e+06
>> Maximum force =  6.7453154e+03 on atom 18769
>> Norm of force =  3.3632809e+01
>>
>> Simulation ended prematurely, no performance report will be written.
>>
>>
>> my em.mdp file contains following parameters.
>>
>> integrator=  steep; simulation algorithm
>> dt=  0.002; time step (ps)
>> nsteps=  2000; # steps
>> comm_mode=  linear; c.o.m. motion reset
>> ;
>> ;Energy Minimization
>> emtol=  500; converged F lt value (kJ mol-1 nm-1)
>> emstep=  0.01 ; initial step size (nm)
>> ;
>> ;Output Control
>> nstxout=  5 ; write coordinates to .trr
>> nstvout=  5; write velocities to .trr
>> nstlog=  5; write energies to .log
>> nstenergy=  1; write energies to .edr
>> ;
>> ;Neightbour Searching
>> cutoff-scheme   =  Verlet; scheme used for
>> generating pair list
>> 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)
>> ;
>> ;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
>> ;
>> ;Temperature Coupling
>> Tcoupl=  no; type of temperature coupling
>> ;
>> ;Pressure Coupling
>> Pcoupl=  no ; type of pressure coupling
>> ;
>> ;Velocity Generation
>> gen_vel=  no ; generate initial velocities
>> ;
>> ;Bonds
>> constraints=  none; bond constraint type
>>
>> I used gmx solvate to add water molecules to the system.
>>
>> How could I get rid of bad contacts of water molecules? Appreciate if
>> anyone help me to solve the problem.
>>
>
> mdrun stopped after 2000 steps because you told it to. You need to
> minimize further, so increase nsteps (or set it to -1 to let mdrun go as
> long as it needs to without having to guess a number).
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> 

Re: [gmx-users] Energy Minimization Error

[Justin Lemkul]

On 10/19/17 8:10 PM, Amali Guruge wrote:

Dear Gromacs Users,

I tried to energy minimize my system using the steep integrator. However,
it gave the following message.

Steepest Descents:
Tolerance (Fmax)   =  5.0e+02
Number of steps= 2000
Step=0, Dmax= 1.0e-02 nm, Epot=  3.96157e+06 Fmax= 1.00697e+06, atom=
14611
Step=1, Dmax= 1.0e-02 nm, Epot=  2.99970e+06 Fmax= 4.04778e+05, atom=
18527
Step=2, Dmax= 1.2e-02 nm, Epot=  1.54766e+06 Fmax= 1.52387e+05, atom=
1005
Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom=
6994
Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom=
58902
Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom=
515
Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom=
188631
Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom=
188631
Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom=
188631
Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom=
188631
Step=   10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom=
188631

step 11: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

After 2000 steps it says,

Steepest Descents did not converge to Fmax < 500 in 2001 steps.
Potential Energy  = -4.6310655e+06
Maximum force =  6.7453154e+03 on atom 18769
Norm of force =  3.3632809e+01

Simulation ended prematurely, no performance report will be written.


my em.mdp file contains following parameters.

integrator=  steep; simulation algorithm
dt=  0.002; time step (ps)
nsteps=  2000; # steps
comm_mode=  linear; c.o.m. motion reset
;
;Energy Minimization
emtol=  500; converged F lt value (kJ mol-1 nm-1)
emstep=  0.01 ; initial step size (nm)
;
;Output Control
nstxout=  5 ; write coordinates to .trr
nstvout=  5; write velocities to .trr
nstlog=  5; write energies to .log
nstenergy=  1; write energies to .edr
;
;Neightbour Searching
cutoff-scheme   =  Verlet; scheme used for
generating pair list
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)
;
;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
;
;Temperature Coupling
Tcoupl=  no; type of temperature coupling
;
;Pressure Coupling
Pcoupl=  no ; type of pressure coupling
;
;Velocity Generation
gen_vel=  no ; generate initial velocities
;
;Bonds
constraints=  none; bond constraint type

I used gmx solvate to add water molecules to the system.

How could I get rid of bad contacts of water molecules? Appreciate if
anyone help me to solve the problem.


mdrun stopped after 2000 steps because you told it to. You need to 
minimize further, so increase nsteps (or set it to -1 to let mdrun go as 
long as it needs to without having to guess a number).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Gromacs Users mailing list

* Please search the archive at 
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* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] energy minimization error

[faride badalkhani]

Hi,

Thanks a lot for your time and patience. This time, I chose a very simple
structure and then inspected the generated topology. The interesting point
was that, there were some missing interactions. When I inspected them. I
found that I had defined those interactions in ffbonded.itp file, but
pdb2gmx has not assigned those definitions to these interactions. However,
I added the appropriate gb_, ga_, or gd_ manually, and then performed the
MD simulations and received an error as follows:

Step=  210, Dmax= 6.6e-03 nm, Epot= -8.80977e+04 Fmax= 1.48278e+05, atom= 46
Step=  212, Dmax= 4.0e-03 nm, Epot= -8.90453e+04 Fmax= 1.76644e+05, atom= 44
Step=  216, Dmax= 5.9e-04 nm, Epot= -8.90760e+04 Fmax= 1.48643e+05, atom= 46
Step=  218, Dmax= 3.6e-04 nm, Epot= -8.91295e+04 Fmax= 1.75349e+05, atom= 44
Step=  221, Dmax= 1.1e-04 nm, Epot= -8.91493e+04 Fmax= 1.48437e+05, atom= 46
Step=  224, Dmax= 3.2e-05 nm, Epot= -8.91556e+04 Fmax= 1.74146e+05, atom= 44
Step=  227, Dmax= 9.6e-06 nm, Epot= -8.91559e+04 Fmax= 1.51118e+05, atom= 46
Step=  229, Dmax= 5.8e-06 nm, Epot= -8.91570e+04 Fmax= 1.71312e+05, atom= 44
Step=  232, Dmax= 1.7e-06 nm, Epot= -8.91571e+04 Fmax= 1.54271e+05, atom= 46
Step=  234, Dmax= 1.0e-06 nm, Epot= -8.91572e+04 Fmax= 1.70893e+05, atom= 44
Step=  235, Dmax= 1.2e-06 nm, Epot= -8.91570e+04 Fmax= 1.57473e+05, atom= 46
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 100 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 236 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -8.9157188e+04
Maximum force =  1.7089320e+05 on atom 44
Norm of force =  3.3110510e+03

gcq#220: "Let's Go Hang Out In a Mall" (LIVE)

farideh@farideh-P61A-D3:~/multiple/G0$

you can access all the files via the following link:
https://www.dropbox.com/s/m1kxafyu1n749hb/G0.zip?dl=0

Truly yours,
Farideh

On Thu, Oct 22, 2015 at 11:24 AM, Mark Abraham 
wrote:

> Hi,
>
> Did you inspect your topology like I suggested? You need to know that there
> are bonds exactly where you intend them, before doing any calculations with
> them.
>
> Mark
>
> On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani <
> farideh.kham...@gmail.com>
> wrote:
>
> > Hi,
> >
> > I am trying to simulate a hyper-branched polymer (a dendrimer) in water.
> > But, every time the system blows up at energy minimization step.
> Therefore,
> > according to what Mark had recommended I decided to start with a much
> > smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had
> > optimized it at M062x/6-31G* level, before starting the MD simulations.
> > Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
> > residue by residue. After that, I started simulation procedure and
> > continued step by step. In spite of G3 PAMAM dendrimer I didn't face any
> > errors in energy minimization step, and the potential energy - EM step
> plot
> > was reasonable. But, when I loaded em.gro file in VMD, the structure was
> > completely messed up as in G3 dendrimer. This time I continued the MD
> > simulation until production MD, and there was no error. However, the
> system
> > is blown up. You can access all the simulation files, pdb structure, and
> > the photos of G1 structure before and after EM step via:
> >
> > https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0
> >
> > Since I am a beginner in this area, I do not know what is the solution
> for
> > this problem.
> > Do you think errors that occur during the G3 simulation are relevant to
> the
> > initial structure?
> > any suggestion or recommendation is appreciated.
> >
> > Thanks in advance
> > Farideh
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] energy minimization error

[Mark Abraham]

Hi,

pdb2gmx and grompp are pretty talkative about things like missing
parameters and bonds - go back and read what they had to say, and
particularly what pdb2gmx thought about your specbonds.

Mark

On Fri, Oct 23, 2015 at 5:51 PM faride badalkhani 
wrote:

> Hi,
>
> Thanks a lot for your time and patience. This time, I chose a very simple
> structure and then inspected the generated topology. The interesting point
> was that, there were some missing interactions. When I inspected them. I
> found that I had defined those interactions in ffbonded.itp file, but
> pdb2gmx has not assigned those definitions to these interactions. However,
> I added the appropriate gb_, ga_, or gd_ manually, and then performed the
> MD simulations and received an error as follows:
>
> Step=  210, Dmax= 6.6e-03 nm, Epot= -8.80977e+04 Fmax= 1.48278e+05, atom=
> 46
> Step=  212, Dmax= 4.0e-03 nm, Epot= -8.90453e+04 Fmax= 1.76644e+05, atom=
> 44
> Step=  216, Dmax= 5.9e-04 nm, Epot= -8.90760e+04 Fmax= 1.48643e+05, atom=
> 46
> Step=  218, Dmax= 3.6e-04 nm, Epot= -8.91295e+04 Fmax= 1.75349e+05, atom=
> 44
> Step=  221, Dmax= 1.1e-04 nm, Epot= -8.91493e+04 Fmax= 1.48437e+05, atom=
> 46
> Step=  224, Dmax= 3.2e-05 nm, Epot= -8.91556e+04 Fmax= 1.74146e+05, atom=
> 44
> Step=  227, Dmax= 9.6e-06 nm, Epot= -8.91559e+04 Fmax= 1.51118e+05, atom=
> 46
> Step=  229, Dmax= 5.8e-06 nm, Epot= -8.91570e+04 Fmax= 1.71312e+05, atom=
> 44
> Step=  232, Dmax= 1.7e-06 nm, Epot= -8.91571e+04 Fmax= 1.54271e+05, atom=
> 46
> Step=  234, Dmax= 1.0e-06 nm, Epot= -8.91572e+04 Fmax= 1.70893e+05, atom=
> 44
> Step=  235, Dmax= 1.2e-06 nm, Epot= -8.91570e+04 Fmax= 1.57473e+05, atom=
> 46
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 100 (which may not be possible for your system).
> It stopped because the algorithm tried to make a new step whose size was
> too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 236 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  = -8.9157188e+04
> Maximum force =  1.7089320e+05 on atom 44
> Norm of force =  3.3110510e+03
>
> gcq#220: "Let's Go Hang Out In a Mall" (LIVE)
>
> farideh@farideh-P61A-D3:~/multiple/G0$
>
> you can access all the files via the following link:
> https://www.dropbox.com/s/m1kxafyu1n749hb/G0.zip?dl=0
>
> Truly yours,
> Farideh
>
> On Thu, Oct 22, 2015 at 11:24 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Did you inspect your topology like I suggested? You need to know that
> there
> > are bonds exactly where you intend them, before doing any calculations
> with
> > them.
> >
> > Mark
> >
> > On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani <
> > farideh.kham...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > I am trying to simulate a hyper-branched polymer (a dendrimer) in
> water.
> > > But, every time the system blows up at energy minimization step.
> > Therefore,
> > > according to what Mark had recommended I decided to start with a much
> > > smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I
> had
> > > optimized it at M062x/6-31G* level, before starting the MD simulations.
> > > Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
> > > residue by residue. After that, I started simulation procedure and
> > > continued step by step. In spite of G3 PAMAM dendrimer I didn't face
> any
> > > errors in energy minimization step, and the potential energy - EM step
> > plot
> > > was reasonable. But, when I loaded em.gro file in VMD, the structure
> was
> > > completely messed up as in G3 dendrimer. This time I continued the MD
> > > simulation until production MD, and there was no error. However, the
> > system
> > > is blown up. You can access all the simulation files, pdb structure,
> and
> > > the photos of G1 structure before and after EM step via:
> > >
> > > https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0
> > >
> > > Since I am a beginner in this area, I do not know what is the solution
> > for
> > > this problem.
> > > Do you think errors that occur during the G3 simulation are relevant to
> > the
> > > initial structure?
> > > any suggestion or recommendation is appreciated.
> > >
> > > Thanks in advance
> > > Farideh
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * 

Re: [gmx-users] energy minimization error

[Mark Abraham]

Hi,

Did you inspect your topology like I suggested? You need to know that there
are bonds exactly where you intend them, before doing any calculations with
them.

Mark

On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani 
wrote:

> Hi,
>
> I am trying to simulate a hyper-branched polymer (a dendrimer) in water.
> But, every time the system blows up at energy minimization step. Therefore,
> according to what Mark had recommended I decided to start with a much
> smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had
> optimized it at M062x/6-31G* level, before starting the MD simulations.
> Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
> residue by residue. After that, I started simulation procedure and
> continued step by step. In spite of G3 PAMAM dendrimer I didn't face any
> errors in energy minimization step, and the potential energy - EM step plot
> was reasonable. But, when I loaded em.gro file in VMD, the structure was
> completely messed up as in G3 dendrimer. This time I continued the MD
> simulation until production MD, and there was no error. However, the system
> is blown up. You can access all the simulation files, pdb structure, and
> the photos of G1 structure before and after EM step via:
>
> https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0
>
> Since I am a beginner in this area, I do not know what is the solution for
> this problem.
> Do you think errors that occur during the G3 simulation are relevant to the
> initial structure?
> any suggestion or recommendation is appreciated.
>
> Thanks in advance
> Farideh
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Energy minimization error

[faride badalkhani]

Hi,

As you said, I started with a G1 PAMAM dendrimer, rather than a G3 one. I
had optimized it at M062x/6-31G* level, before starting the MD simulations.
Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
residue by residue. After that, I started simulation procedure and
continued step by step. In spite of G3 PAMAM dendrimer I didn't face any
errors in energy minimization step, and the potential energy - EM step plot
was reasonable. But, when I loaded em.gro file in VMD, the structure was
completely messed up as in G3 dendrimer. This time I continued the MD
simulation until production MD, and there was no error. However, the system
is blown up. You can access all the simulation files, pdb structure, and
the photos of G1 structure before and after EM step via:

https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0

Since I am a beginner in this area, I do not know what is the solution for
this problem.
Do you think errors that occur during the G3 simulation are relevant to the
initial structure?
any suggestion or recommendation is appreciated.

Thanks in advance
Farideh

On Sat, Oct 17, 2015 at 6:29 PM, Mark Abraham 
wrote:

> Hi,
>
> What some visualization program shows about bonds doesn't mean anything -
> it has not parsed your topology. You have no option but to look at the .top
> produced and reason about what it shows, but yours is very complex. I
> strongly recommend starting with something simpler than a multiply branched
> dendrimer. Join two units with a specbond, inspect the .top so that you
> know it has what you think it has, and get that to EM and simulation
> stably. Then you can get more complex.
>
> Mark
>
> On Sat, Oct 17, 2015 at 3:58 PM faride badalkhani <
> farideh.kham...@gmail.com>
> wrote:
>
> > Dear gromacs users,
> >
> > As I said before I faced with the minimization error, so I changed
> > coordinates of atoms in pdb file, but the problem is the same. the only
> > thing that changes in every run is atom number. I modified pdb for many
> > times.
> >
> > Steepest Descents converged to Fmax < 1000 in 530 steps
> > Potential Energy  = -5.5180181e+05
> > Maximum force =  7.4496063e+02 on atom 501
> > Norm of force =  3.8248455e+01
> >
> >
> > Moreover gro structure was completely messed up when was visualized in
> vmd.
> > you can see the picture of my structure in below dropbox link:
> >
> > https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0
> > https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0
> >
> > and this is the pdb file dropbox link:
> >
> > https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0
> >
> >
> > I used cg algorithm after steep for minimization, too. But it did not
> work.
> > is there any way to solve this problem?
> >
> > any help is appreciated.
> >
> > On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Look at atom 380 and see why the forces might be high.
> > >
> > > Mark
> > >
> > > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <
> > > farideh.kham...@gmail.com>
> > > wrote:
> > >
> > > > Thank you for your great help on specbond.dat file. I defined it and
> I
> > > > could go ahead until Energy minimization step. I have used this
> > minim.mdp
> > > > file
> > > >
> > > > ; minim.mdp - used as input into grompp to generate em.tpr
> > > > ; Parameters describing what to do, when to stop and what to save
> > > > integrator= steep; Algorithm (steep = steepest descent
> > > > minimization)
> > > > emtol  = 1000.0  ; Stop minimization when the maximum
> > force <
> > > > 1000.0 kJ/mol/nm
> > > > emstep   = 0.01  ; Energy step size
> > > > nsteps= 5  ; Maximum number of (minimization)
> steps
> > > to
> > > > perform
> > > >
> > > > ; Parameters describing how to find the neighbors of each atom and
> how
> > to
> > > > calculate the interactions
> > > > nstlist  = 1; Frequency to update the neighbor
> list
> > > and
> > > > long range forces
> > > > ns_type   = grid; Method to determine neighbor list
> > > > (simple, grid)
> > > > rlist = 1.0; Cut-off for making neighbor list
> > > > (short range forces)
> > > > coulombtype= PME; Treatment of long range electrostatic
> > > > interactions
> > > > rcoulomb = 1.0; Short-range electrostatic cut-off
> > > > rvdw   = 1.0; Short-range Van der Waals cut-off
> > > > pbc = xyz ; Periodic Boundary Conditions
> > (yes/no)
> > > >
> > > > But when I run mdrun -v -deffnm em command, I get this error:
> > > >
> > > > Energy minimization has stopped, but the forces have not converged to
> > the
> > > > requested precision Fmax < 1000 (which may not be possible for your
> > > > system).
> > > > It stopped because the algorithm tried to make a new step whose size
> > was
> > > > too
> > > > small, or there was no change 

Re: [gmx-users] Energy minimization error

[faride badalkhani]

Dear gromacs users,

As I said before I faced with the minimization error, so I changed
coordinates of atoms in pdb file, but the problem is the same. the only
thing that changes in every run is atom number. I modified pdb for many
times.

Steepest Descents converged to Fmax < 1000 in 530 steps
Potential Energy  = -5.5180181e+05
Maximum force =  7.4496063e+02 on atom 501
Norm of force =  3.8248455e+01


Moreover gro structure was completely messed up when was visualized in vmd.
you can see the picture of my structure in below dropbox link:

https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0
https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0

and this is the pdb file dropbox link:

https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0


I used cg algorithm after steep for minimization, too. But it did not work.
is there any way to solve this problem?

any help is appreciated.

On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham 
wrote:

> Hi,
>
> Look at atom 380 and see why the forces might be high.
>
> Mark
>
> On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <
> farideh.kham...@gmail.com>
> wrote:
>
> > Thank you for your great help on specbond.dat file. I defined it and I
> > could go ahead until Energy minimization step. I have used this minim.mdp
> > file
> >
> > ; minim.mdp - used as input into grompp to generate em.tpr
> > ; Parameters describing what to do, when to stop and what to save
> > integrator= steep; Algorithm (steep = steepest descent
> > minimization)
> > emtol  = 1000.0  ; Stop minimization when the maximum force <
> > 1000.0 kJ/mol/nm
> > emstep   = 0.01  ; Energy step size
> > nsteps= 5  ; Maximum number of (minimization) steps
> to
> > perform
> >
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the interactions
> > nstlist  = 1; Frequency to update the neighbor list
> and
> > long range forces
> > ns_type   = grid; Method to determine neighbor list
> > (simple, grid)
> > rlist = 1.0; Cut-off for making neighbor list
> > (short range forces)
> > coulombtype= PME; Treatment of long range electrostatic
> > interactions
> > rcoulomb = 1.0; Short-range electrostatic cut-off
> > rvdw   = 1.0; Short-range Van der Waals cut-off
> > pbc = xyz ; Periodic Boundary Conditions (yes/no)
> >
> > But when I run mdrun -v -deffnm em command, I get this error:
> >
> > Energy minimization has stopped, but the forces have not converged to the
> > requested precision Fmax < 1000 (which may not be possible for your
> > system).
> > It stopped because the algorithm tried to make a new step whose size was
> > too
> > small, or there was no change in the energy since last step. Either way,
> we
> > regard the minimization as converged to within the available machine
> > precision, given your starting configuration and EM parameters.
> >
> > Double precision normally gives you higher accuracy, but this is often
> not
> > needed for preparing to run molecular dynamics.
> > You might need to increase your constraint accuracy, or turn
> > off constraints altogether (set constraints = none in mdp file)
> >
> > writing lowest energy coordinates.
> >
> > Steepest Descents converged to machine precision in 90 steps,
> > but did not reach the requested Fmax < 1000.
> > Potential Energy  = -2.3956744e+05
> > Maximum force =  1.5824519e+05 on atom 380
> > Norm of force =  1.7695243e+03
> >
> > gcq#187: "Been There, Done It" (Beavis and Butthead)
> >
> > farideh@farideh-P61A-D3:~/FARIDEH$
> >
> > I changed the emtol, emstep, and nsteps for a few times. However, I
> > couldn't resolve this problem. Could you tell me if there is something
> > wrong with the minim.mdp file?
> >
> > You can see all the files via:
> > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0
> >
> > Truly yours,
> > Farideh
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read 

Re: [gmx-users] Energy minimization error

[Mark Abraham]

Hi,

What some visualization program shows about bonds doesn't mean anything -
it has not parsed your topology. You have no option but to look at the .top
produced and reason about what it shows, but yours is very complex. I
strongly recommend starting with something simpler than a multiply branched
dendrimer. Join two units with a specbond, inspect the .top so that you
know it has what you think it has, and get that to EM and simulation
stably. Then you can get more complex.

Mark

On Sat, Oct 17, 2015 at 3:58 PM faride badalkhani 
wrote:

> Dear gromacs users,
>
> As I said before I faced with the minimization error, so I changed
> coordinates of atoms in pdb file, but the problem is the same. the only
> thing that changes in every run is atom number. I modified pdb for many
> times.
>
> Steepest Descents converged to Fmax < 1000 in 530 steps
> Potential Energy  = -5.5180181e+05
> Maximum force =  7.4496063e+02 on atom 501
> Norm of force =  3.8248455e+01
>
>
> Moreover gro structure was completely messed up when was visualized in vmd.
> you can see the picture of my structure in below dropbox link:
>
> https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0
> https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0
>
> and this is the pdb file dropbox link:
>
> https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0
>
>
> I used cg algorithm after steep for minimization, too. But it did not work.
> is there any way to solve this problem?
>
> any help is appreciated.
>
> On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Look at atom 380 and see why the forces might be high.
> >
> > Mark
> >
> > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <
> > farideh.kham...@gmail.com>
> > wrote:
> >
> > > Thank you for your great help on specbond.dat file. I defined it and I
> > > could go ahead until Energy minimization step. I have used this
> minim.mdp
> > > file
> > >
> > > ; minim.mdp - used as input into grompp to generate em.tpr
> > > ; Parameters describing what to do, when to stop and what to save
> > > integrator= steep; Algorithm (steep = steepest descent
> > > minimization)
> > > emtol  = 1000.0  ; Stop minimization when the maximum
> force <
> > > 1000.0 kJ/mol/nm
> > > emstep   = 0.01  ; Energy step size
> > > nsteps= 5  ; Maximum number of (minimization) steps
> > to
> > > perform
> > >
> > > ; Parameters describing how to find the neighbors of each atom and how
> to
> > > calculate the interactions
> > > nstlist  = 1; Frequency to update the neighbor list
> > and
> > > long range forces
> > > ns_type   = grid; Method to determine neighbor list
> > > (simple, grid)
> > > rlist = 1.0; Cut-off for making neighbor list
> > > (short range forces)
> > > coulombtype= PME; Treatment of long range electrostatic
> > > interactions
> > > rcoulomb = 1.0; Short-range electrostatic cut-off
> > > rvdw   = 1.0; Short-range Van der Waals cut-off
> > > pbc = xyz ; Periodic Boundary Conditions
> (yes/no)
> > >
> > > But when I run mdrun -v -deffnm em command, I get this error:
> > >
> > > Energy minimization has stopped, but the forces have not converged to
> the
> > > requested precision Fmax < 1000 (which may not be possible for your
> > > system).
> > > It stopped because the algorithm tried to make a new step whose size
> was
> > > too
> > > small, or there was no change in the energy since last step. Either
> way,
> > we
> > > regard the minimization as converged to within the available machine
> > > precision, given your starting configuration and EM parameters.
> > >
> > > Double precision normally gives you higher accuracy, but this is often
> > not
> > > needed for preparing to run molecular dynamics.
> > > You might need to increase your constraint accuracy, or turn
> > > off constraints altogether (set constraints = none in mdp file)
> > >
> > > writing lowest energy coordinates.
> > >
> > > Steepest Descents converged to machine precision in 90 steps,
> > > but did not reach the requested Fmax < 1000.
> > > Potential Energy  = -2.3956744e+05
> > > Maximum force =  1.5824519e+05 on atom 380
> > > Norm of force =  1.7695243e+03
> > >
> > > gcq#187: "Been There, Done It" (Beavis and Butthead)
> > >
> > > farideh@farideh-P61A-D3:~/FARIDEH$
> > >
> > > I changed the emtol, emstep, and nsteps for a few times. However, I
> > > couldn't resolve this problem. Could you tell me if there is something
> > > wrong with the minim.mdp file?
> > >
> > > You can see all the files via:
> > > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0
> > >
> > > Truly yours,
> > > Farideh
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > 

Re: [gmx-users] Energy minimization error

[Mark Abraham]

Hi,

Look at atom 380 and see why the forces might be high.

Mark

On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani 
wrote:

> Thank you for your great help on specbond.dat file. I defined it and I
> could go ahead until Energy minimization step. I have used this minim.mdp
> file
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator= steep; Algorithm (steep = steepest descent
> minimization)
> emtol  = 1000.0  ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> emstep   = 0.01  ; Energy step size
> nsteps= 5  ; Maximum number of (minimization) steps to
> perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist  = 1; Frequency to update the neighbor list and
> long range forces
> ns_type   = grid; Method to determine neighbor list
> (simple, grid)
> rlist = 1.0; Cut-off for making neighbor list
> (short range forces)
> coulombtype= PME; Treatment of long range electrostatic
> interactions
> rcoulomb = 1.0; Short-range electrostatic cut-off
> rvdw   = 1.0; Short-range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions (yes/no)
>
> But when I run mdrun -v -deffnm em command, I get this error:
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 1000 (which may not be possible for your
> system).
> It stopped because the algorithm tried to make a new step whose size was
> too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 90 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -2.3956744e+05
> Maximum force =  1.5824519e+05 on atom 380
> Norm of force =  1.7695243e+03
>
> gcq#187: "Been There, Done It" (Beavis and Butthead)
>
> farideh@farideh-P61A-D3:~/FARIDEH$
>
> I changed the emtol, emstep, and nsteps for a few times. However, I
> couldn't resolve this problem. Could you tell me if there is something
> wrong with the minim.mdp file?
>
> You can see all the files via:
> https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0
>
> Truly yours,
> Farideh
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>
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Re: [gmx-users] energy minimization error

[James Lord]

Hi Justin
For now I  used


*mdrun -nt 1*


* and got rid of this error so hopefully the simulation wont crash. *

*Cheers*

*James*


On Sat, Jun 27, 2015 at 11:19 AM, James Lord jjamesgreen...@gmail.com
wrote:

 Hi Justin,
 I have asked this before, but this time I started up from scratch and used
 the input files that I know they are fine but again I am getting this
 error, Would you please tell me what is wrong in my topology files and
 where about in .top files the bond length are defined?


 https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing

 Cheers
 James

 On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 5/16/15 11:35 PM, James Lord wrote:

 Hi Justin
 Thanks for this. Can you tell me which step(s) this bond length is
 defined
 What should I do (redo) to resolve this issue?


 The bonds are defined in the topology.  The DD algorithm reads what's in
 the coordinate file and builds cells based on the geometry it finds there.

 Without a full description of what's in your system, what steps you've
 taken to prepare it (full commands, in order), there's little I can suggest
 because it would all be guesswork.


 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
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 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

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Re: [gmx-users] energy minimization error

[Justin Lemkul]

On 6/27/15 2:29 AM, James Lord wrote:

Hi Justin
For now I  used


*mdrun -nt 1*


* and got rid of this error so hopefully the simulation wont crash. *



The DD errors have nothing to do with physical stability; you just can't 
necessarily parallelize any arbitrary system over any arbitrary number of cores 
(DD cells).  You can also parallelize with OpenMP to get some speed-up (mdrun 
-ntmpi 1 -ntomp N).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization error

[Justin Lemkul]

On 6/26/15 7:19 PM, James Lord wrote:

Hi Justin,
I have asked this before, but this time I started up from scratch and used
the input files that I know they are fine but again I am getting this
error, Would you please tell me what is wrong in my topology files and
where about in .top files the bond length are defined?

https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing



There's nothing I can do with a topology that's a series of #include statements.

Please also remind me what this is all about so I don't have to go digging 
through the archives for something from a month ago.  Lots of things have 
happened since then :)


-Justin


Cheers
James

On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote:




On 5/16/15 11:35 PM, James Lord wrote:


Hi Justin
Thanks for this. Can you tell me which step(s) this bond length is
defined
What should I do (redo) to resolve this issue?



The bonds are defined in the topology.  The DD algorithm reads what's in
the coordinate file and builds cells based on the geometry it finds there.

Without a full description of what's in your system, what steps you've
taken to prepare it (full commands, in order), there's little I can suggest
because it would all be guesswork.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization error

[James Lord]

Hi Justin,
I have asked this before, but this time I started up from scratch and used
the input files that I know they are fine but again I am getting this
error, Would you please tell me what is wrong in my topology files and
where about in .top files the bond length are defined?

https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing

Cheers
James

On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 5/16/15 11:35 PM, James Lord wrote:

 Hi Justin
 Thanks for this. Can you tell me which step(s) this bond length is
 defined
 What should I do (redo) to resolve this issue?


 The bonds are defined in the topology.  The DD algorithm reads what's in
 the coordinate file and builds cells based on the geometry it finds there.

 Without a full description of what's in your system, what steps you've
 taken to prepare it (full commands, in order), there's little I can suggest
 because it would all be guesswork.


 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
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Re: [gmx-users] energy minimization error

[Justin Lemkul]

On 5/16/15 11:35 PM, James Lord wrote:

Hi Justin
Thanks for this. Can you tell me which step(s) this bond length is defined
What should I do (redo) to resolve this issue?


The bonds are defined in the topology.  The DD algorithm reads what's in the 
coordinate file and builds cells based on the geometry it finds there.


Without a full description of what's in your system, what steps you've taken to 
prepare it (full commands, in order), there's little I can suggest because it 
would all be guesswork.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Gromacs Users mailing list

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Re: [gmx-users] energy minimization error

[Justin Lemkul]

On 5/16/15 6:27 AM, James Lord wrote:

Dear gmx users,
I am getting this error, Can anyone help me to get around this?
Cheers
James


Program mdrun, VERSION 4.6.3
Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the
given box and a minimum cell size of 6.93203 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition



Log file opened on Sat May 16 22:15:44 2015
Host: james-E530  pid: 22300  nodeid: 0  nnodes:  1
Gromacs version:VERSION 4.6.3
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled
GPU support:disabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration:   AVX_256
FFT library:fftw-3.3.2-sse2
Large file support: enabled
RDTSCP usage:   enabled
Built on:   Wed Oct 30 18:28:46 NZDT 2013
Built by:   james@james-E530 [CMAKE]
Build OS/arch:  Linux 3.11.0-12-generic x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Core(TM) i7-3632QM CPU @ 2.20GHz
Build CPU family:   6   Model: 58   Stepping: 9
Build CPU features: apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1
sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1
C compiler flags:   -mavx-Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter
-Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
-DNDEBUG


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

   Gromacs Runs On Most of All Computer Systems

 :-)  VERSION 4.6.3  (-:

 Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
  Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
 Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
 Michael Shirts, Alfons Sijbers, Peter Tieleman,

Berk Hess, David van der Spoel, and Erik Lindahl.

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  Copyright (c) 2001-2012,2013, The GROMACS development team at
 Uppsala University  The Royal Institute of Technology, Sweden.
 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 Lesser General Public License
 as published by the Free Software Foundation; either version 2.1
  of the License, or (at your option) any later version.

 :-)  mdrun  (-:


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
  --- Thank You ---  

Input Parameters:
integrator   = steep
nsteps   = 5
init-step= 0
cutoff-scheme= Group
ns_type  = Grid
nstlist  = 5
ndelta   = 2
nstcomm  = 100
comm-mode= Linear
nstlog   = 1000
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstcalcenergy= 100
nstenergy= 1000
nstxtcout= 0
init-t   = 0
delta-t  = 0.001
xtcprec  = 1000
fourierspacing   = 0.12
nkx  = 56
nky  = 56
nkz  = 144
pme-order= 4
ewald-rtol   = 1e-05
ewald-geometry   = 0
epsilon-surface  

Re: [gmx-users] Energy minimization error for electroporation simulation of DPPC membrane

[Justin Lemkul]

On 4/28/15 8:14 AM, Abhijit Jassem wrote:

Hi all,

I am a beginner to GROMACS and MD simulations in general. I’m trying to
model electroporation in a DPPC membrane but I am having issues with the
energy minimization step. I am basing my approach on the one followed in
Dr. Justin Lemkul’s KALP-15 in DPPC Tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html)
but without the steps that use the KALP peptide. After I solvate my
membrane, I am trying to run energy minimization, but my steps are moving
much slower than normal and I get the error Water molecule starting at
atom 109448 can not be settled. Check for bad contacts and/or reduce the


Well, what's going on around atom 109448?


timestep if appropriate.” When I looked this error up, I found that
this suggested that I had a bad starting structure, possibly with atoms
overlapping. Based on this, I assume this error originates when I solvate
my membrane. I am currently using the spc216.gro model. Is this an issue
with my water model or am I doing something else wrong?



There are plenty of potential problems, unfortunately not enough information to 
go on.  Simply using SPC isn't a problem, but something either in the 
configuration or the force field is an issue.  Rather than building a large 
system (you have over 100,000 atoms), do something small, like the pre-built 
DPPC bilayer that the tutorial uses.  That's a sanity check.  If that minimizes 
and equilibrates well, that means the force field is fine and something is wrong 
with the way you built your larger system.  If you want help with that, you have 
to tell us exactly what you're doing (exact command sequence).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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