Re: [gmx-users] Minimization problem

[Mark Abraham]

Hi,

You're also using tabulated VDW interactions, so I'd start by looking at
that. What steps have you taken to ensure that each of your topologies
works, e.g. on their own in vacuum?

Mark

On Tue, Jan 9, 2018 at 11:46 PM Neda Rafiee  wrote:

> Dear Users,
> I have a problem in energy minimization step. Actually I have some groups
> of atoms that are freezed and also a chain of protein in water. I want the
> following items:
> constraints =  none
> integrator  =  steep
> emstep  =  0.0001
> emtol   =  500.0
> nsteps  =  50
> ; Neighbor list and pbc's --
> cutoff-scheme   =  group
> nstlist =  1; default is 10 -- try more frequent
> ns_type =  grid ; simple (for no pbc) or grid
> ;
> pbc =  xyz  ; CHANGE
> periodic_molecules  =  no
> ;
> ; Interaction parameters ---
> rlist   =  1
> rlistlong   =  1
> rcoulomb=  1
> ;
> coulombtype =  PME
> epsilon_r   =  1
> ;
> vdwtype =  user; cut-off
> rvdw=  1
>
> but after just 6000 steps it gives me this error:
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 500 (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.
> 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 53429 steps,
> but did not reach the requested Fmax < 500.
> Potential Energy  =  2.46705107676305e+14
> Maximum force =  9.69602643026733e+08 on atom 9415
> Norm of force =  1.70746371816015e+07
>
> Would you please help me understand where the problem is ?!
> Thanks
> Neda
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[gmx-users] Minimization problem

[Neda Rafiee]

Dear Users,
I have a problem in energy minimization step. Actually I have some groups of 
atoms that are freezed and also a chain of protein in water. I want the 
following items:
constraints =  none
integrator  =  steep
emstep  =  0.0001
emtol   =  500.0
nsteps  =  50
; Neighbor list and pbc's --
cutoff-scheme   =  group
nstlist =  1; default is 10 -- try more frequent
ns_type =  grid ; simple (for no pbc) or grid
;
pbc =  xyz  ; CHANGE
periodic_molecules  =  no
;
; Interaction parameters ---
rlist   =  1
rlistlong   =  1
rcoulomb=  1
;
coulombtype =  PME
epsilon_r   =  1
;
vdwtype =  user; cut-off
rvdw=  1 

but after just 6000 steps it gives me this error:
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 500 (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.
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 53429 steps,
but did not reach the requested Fmax < 500.
Potential Energy  =  2.46705107676305e+14
Maximum force =  9.69602643026733e+08 on atom 9415
Norm of force =  1.70746371816015e+07

Would you please help me understand where the problem is ?!
Thanks
Neda
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Re: [gmx-users] Minimization Problem

[Dallas Warren]

Where did you obtain the topology from? What forcefield is it meant to
be used with?  Does that forcefield include bonds between those atom
types?

The error is occurring because when grompp goes through the topology,
it cannot match up the atom types that are bonded together, with an
existing bond within the forcefield.

Easiest solution is to get a topology for that molecule, for the
forcefield you want to use, that someone else has built. Or you could
specify that bonds yourself within the topology.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 10 October 2017 at 04:55, Ednilsom Orestes  wrote:
> Dear Gromacs community
>
> I am trying to run a simulation of choline molecule but found various
> errors concerning to bonds, angles and dihedrals during the minimization.
>
>
>
> Part of the top file (line number in the first column):
> ...
> 29 [ bonds ]
> 30;  aiaj funct
> 311  4 1; N   CT3
> 32114 1; N   CT4
> 331  2 1; N   CT1
> 341  3 1; N   CT2
> 35212 1;   CT1  HC12
> 36213 1;   CT1  HC11
> 37211 1;   CT1  HC13
> 383  7 1;   CT2  HC21
> 393  6 1;   CT2  HC22
> 403  5 1;   CT2  HC23
> 414  8 1;   CT3  HC31
> 42410 1;   CT3  HC32
> 434  9 1;   CT3  HC33
> 44   1417 1;   CT4  HC41
> 45   1415 1;   CT4   CT5
> 46   1416 1;   CT4  HC42
> 47   1520 1;   CT5  HC51
> 48   1518 1;   CT5OH
> 49   1519 1;   CT5  HC52
> 50   2118 1;HOOH
> ...
>
>
> Errors:
>
> ERROR 1 [file topol_choline.top, line 49]:
> No Default Bond type
>
> ERROR 2 [file topol_choline.top, line50]:
> No Default Bond type
>
> and so on with some of the angles and dihedrals...
>
> Does anybody have a clue on how to fix it?
>
> Thanks in advance.
>
> Ednilsom
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[gmx-users] Minimization Problem

[Ednilsom Orestes]

Dear Gromacs community

I am trying to run a simulation of choline molecule but found various
errors concerning to bonds, angles and dihedrals during the minimization.



Part of the top file (line number in the first column):
...
29 [ bonds ]
30;  aiaj funct
311  4 1; N   CT3
32114 1; N   CT4
331  2 1; N   CT1
341  3 1; N   CT2
35212 1;   CT1  HC12
36213 1;   CT1  HC11
37211 1;   CT1  HC13
383  7 1;   CT2  HC21
393  6 1;   CT2  HC22
403  5 1;   CT2  HC23
414  8 1;   CT3  HC31
42410 1;   CT3  HC32
434  9 1;   CT3  HC33
44   1417 1;   CT4  HC41
45   1415 1;   CT4   CT5
46   1416 1;   CT4  HC42
47   1520 1;   CT5  HC51
48   1518 1;   CT5OH
49   1519 1;   CT5  HC52
50   2118 1;HOOH
...


Errors:

ERROR 1 [file topol_choline.top, line 49]:
No Default Bond type

ERROR 2 [file topol_choline.top, line50]:
No Default Bond type

and so on with some of the angles and dihedrals...

Does anybody have a clue on how to fix it?

Thanks in advance.

Ednilsom
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