[gmx-users] simulation using tabulated dihedral potentials.

[Chandan Choudhury]

I am facing some weird problem while using tabulated potentials (esp.
dihedral tabulated potentials) in gromacs 4.6.3. I am trying to generate a
coarse grained (CG) trajectory using the tabulated potentials generated for
the atomistic simulations using VOTCA.

When I donot use the dihedral tabulated potentials, the simulations seems
to proceed smoothly. The problem arises when the dihedral potentials are
incorporated. I have added a link of all the files generated during the
undermentioned runs (https://www.dropbox.com/s/yumzdufuys1ifdr/with-dih.tar)
. It also includes the input files. Here, I list the problem and how do
they occur :

1. $mdrun_463 -v -nice 0 -cpt 1 -cpi state.cpt -nt 2 -pin on (1st Run) >&
ver1.txt
Progress smoothly for few steps (step 536400). Shows the following error :

A list of missing interactions:
           Tab. Dih. of    720 missing      1

Molecule type 'POLCAR'
the first 10 missing interactions, except for exclusions:
           Tab. Dih. atoms    6    7    8    9 global   858   859   860
861

-------------------------------------------------------
Program mdrun_463, VERSION 4.6.3
Source code file: /tmp/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393

Fatal error:
1 of the 2400 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Sometimes Life is Obscene" (Black Crowes

2. Then I continue the run using the state.cpt file
       $mdrun_463 -v -nice 0 -cpt 1 -cpi state.cpt -nt 2 -pin on >& ver2.txt

Further progressed for few more steps (step 973100). Following error is
produced here:

A list of missing interactions:
         Tab. Angles of    800 missing      1
           Tab. Dih. of    720 missing      1

Molecule type 'POLCAR'
the first 10 missing interactions, except for exclusions:
           Tab. Dih. atoms    9   10   11   12 global   237   238   239
240
         Tab. Angles atoms   10   11   12      global   238   239   240

Back Off! I just backed up dd_dump_err_0_n1.pdb to
./#dd_dump_err_0_n1.pdb.1#

Back Off! I just backed up dd_dump_err_0_n0.pdb to
./#dd_dump_err_0_n0.pdb.1#

-------------------------------------------------------
Program mdrun_463, VERSION 4.6.3
Source code file: /tmp/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393

Fatal error:
2 of the 2400 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"She's a Good Sheila Bruce" (Monty Python)

3. Again continued the simulation
           $mdrun_463 -v -nice 0 -cpt 1 -cpi state.cpt -nt 2 -pin on >&
ver3.txt
            Simulation proceeds for further for step 3692700. The again
crashed with the following output:

A list of missing interactions:
         Tab. Angles of    800 missing      1
           Tab. Dih. of    720 missing      2

Molecule type 'POLCAR'
the first 10 missing interactions, except for exclusions:
           Tab. Dih. atoms    6    7    8    9 global   306   307   308
309
         Tab. Angles atoms    7    8    9      global   307   308   309
           Tab. Dih. atoms    7    8    9   10 global   307   308   309
310

Back Off! I just backed up dd_dump_err_0_n0.pdb to
./#dd_dump_err_0_n0.pdb.2#

Back Off! I just backed up dd_dump_err_0_n1.pdb to
./#dd_dump_err_0_n1.pdb.2#

-------------------------------------------------------
Program mdrun_463, VERSION 4.6.3
Source code file: /tmp/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393

Fatal error:
3 of the 2400 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Though the path of the comet is sure, it's constitution is not" (Peter
Hammill)

In this way the simulations proceed. At the end it finally stops at step
71768380 and no further continuation is possible.
Error at this stage :


Started mdrun on node 0 Mon Dec  9 12:24:52 2013

           Step           Time         Lambda
       71768380   358841.90000        0.00000


   Energies (kJ/mol)
     Tab. Bonds    Tab. Angles      Tab. Dih.        LJ (SR)   Coulomb (SR)
    5.18063e+03    6.57460e+03    8.27504e+02    1.20890e+04    0.00000e+00
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
    2.46717e+04    1.12236e+04    3.58953e+04    9.38392e+02    4.95772e+03

DD  step 71768389 load imb.: force  0.5%


Not all bonded interactions have been properly assigned to the domain
decomposition cells

A list of missing interactions:
           Tab. Dih. of    720 missing      1

Molecule type 'POLCAR'
the first 10 missing interactions, except for exclusions:
           Tab. Dih. atoms    9   10   11   12 global    45    46    47
48

-------------------------------------------------------
Program mdrun_463, VERSION 4.6.3
Source code file: /tmp/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393

Fatal error:
1 of the 2400 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I donot understand why the simulations shows these errors and again it
continues further for few more steps. In the topology file all the
interactions are mentioned.
A point is to be noted here that when I comment the dihedral sections in
the topology the simulation proceeds very smoothly. All the files are
uploaded here (https://www.dropbox.com/s/yumzdufuys1ifdr/with-dih.tar)
I understand from the mailing list, that there are only handful of users
actually using the tabulated potentials.

Any insight will be very helpful.


Chandan


--
Chandan kumar Choudhury
NCL, Pune
INDIA