[gmx-users] Protein-membrane simulation error.

Sat May 21 00:28:41 CEST 2016

Hello,
I received the following error while trying to run "Adding ion" step during
Protein-membrane simulation. Any advice or suggestions will be greatly
appreciated.

ERROR:
Command line:
  gmx grompp -f ions.mdp -c system_box_sol.gro -p topol.top -o ions.tpr

NOTE 1 [file ions.mdp, line 17]:
  ions.mdp did not specify a value for the .mdp option "cutoff-scheme".
  Probably it was first intended for use with GROMACS before 4.6. In 4.6,
  the Verlet scheme was introduced, but the group scheme was still the
  default. The default is now the Verlet scheme, so you will observe
  different behaviour.

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11#

NOTE 2 [file ions.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 1335440429
Generated 968 of the 2016 non-bonded parameter combinations

ERROR 1 [file topol.top, line 765]:
  No default Proper Dih. types

ERROR 2 [file topol.top, line 766]:
  No default Proper Dih. types

ERROR 3 [file topol.top, line 768]:
  No default Proper Dih. types

ERROR 4 [file topol.top, line 769]:
  No default Proper Dih. types

ERROR 5 [file topol.top, line 770]:
  No default Proper Dih. types

ERROR 6 [file topol.top, line 771]:
  No default Proper Dih. types

ERROR 7 [file topol.top, line 772]:
  No default Proper Dih. types

ERROR 8 [file topol.top, line 773]:
  No default Proper Dih. types

ERROR 9 [file topol.top, line 774]:
  No default Proper Dih. types

ERROR 10 [file topol.top, line 776]:
  No default Proper Dih. types

ERROR 11 [file topol.top, line 777]:
  No default Proper Dih. types

ERROR 12 [file topol.top, line 778]:
  No default Proper Dih. types

ERROR 13 [file topol.top, line 779]:
  No default Proper Dih. types

ERROR 14 [file topol.top, line 780]:
  No default Proper Dih. types

ERROR 15 [file topol.top, line 781]:
  No default Proper Dih. types

ERROR 16 [file topol.top, line 782]:
  No default Proper Dih. types

ERROR 17 [file topol.top, line 784]:
  No default Proper Dih. types

ERROR 18 [file topol.top, line 785]:
  No default Proper Dih. types

ERROR 19 [file topol.top, line 786]:
  No default Proper Dih. types

ERROR 20 [file topol.top, line 787]:
  No default Proper Dih. types

ERROR 21 [file topol.top, line 789]:
  No default Proper Dih. types

ERROR 22 [file topol.top, line 790]:
  No default Proper Dih. types

ERROR 23 [file topol.top, line 792]:
  No default Proper Dih. types

ERROR 24 [file topol.top, line 793]:
  No default Proper Dih. types

ERROR 25 [file topol.top, line 794]:
  No default Proper Dih. types

ERROR 26 [file topol.top, line 795]:
  No default Proper Dih. types

ERROR 27 [file topol.top, line 797]:
  No default Proper Dih. types

ERROR 28 [file topol.top, line 798]:
  No default Proper Dih. types

ERROR 29 [file topol.top, line 800]:
  No default Proper Dih. types

ERROR 30 [file topol.top, line 801]:
  No default Proper Dih. types

ERROR 31 [file topol.top, line 802]:
  No default Proper Dih. types

ERROR 32 [file topol.top, line 803]:
  No default Proper Dih. types

ERROR 33 [file topol.top, line 805]:
  No default Proper Dih. types

ERROR 34 [file topol.top, line 806]:
  No default Proper Dih. types

ERROR 35 [file topol.top, line 808]:
  No default Proper Dih. types

ERROR 36 [file topol.top, line 809]:
  No default Proper Dih. types

ERROR 37 [file topol.top, line 810]:
  No default Proper Dih. types

ERROR 38 [file topol.top, line 811]:
  No default Proper Dih. types

ERROR 39 [file topol.top, line 813]:
  No default Proper Dih. types

ERROR 40 [file topol.top, line 814]:
  No default Proper Dih. types

ERROR 41 [file topol.top, line 816]:
  No default Proper Dih. types

ERROR 42 [file topol.top, line 817]:
  No default Proper Dih. types

ERROR 43 [file topol.top, line 818]:
  No default Proper Dih. types

ERROR 44 [file topol.top, line 819]:
  No default Proper Dih. types

ERROR 45 [file topol.top, line 821]:
  No default Proper Dih. types

ERROR 46 [file topol.top, line 822]:
  No default Proper Dih. types

ERROR 47 [file topol.top, line 823]:
  No default Proper Dih. types

ERROR 48 [file topol.top, line 824]:
  No default Proper Dih. types

ERROR 49 [file topol.top, line 825]:
  No default Proper Dih. types

ERROR 50 [file topol.top, line 826]:
  No default Proper Dih. types

ERROR 51 [file topol.top, line 827]:
  No default Proper Dih. types

ERROR 52 [file topol.top, line 829]:
  No default Proper Dih. types

ERROR 53 [file topol.top, line 830]:
  No default Proper Dih. types

ERROR 54 [file topol.top, line 831]:
  No default Proper Dih. types

ERROR 55 [file topol.top, line 832]:
  No default Proper Dih. types

ERROR 56 [file topol.top, line 833]:
  No default Proper Dih. types

ERROR 57 [file topol.top, line 834]:
  No default Proper Dih. types

ERROR 58 [file topol.top, line 835]:
  No default Proper Dih. types

ERROR 59 [file topol.top, line 837]:
  No default Proper Dih. types

ERROR 60 [file topol.top, line 838]:
  No default Proper Dih. types

Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 3 bonded neighbours molecule type 'DPPC'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 3 [file topol.top, line 930]:
  System has non-zero total charge: 4.000000
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.

Removing all charge groups because cutoff-scheme=Verlet

There were 3 notes

-------------------------------------------------------
Program gmx grompp, VERSION 5.1.2
Source code file:
/home/guptalab/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, line: 1738

Fatal error:
There were 60 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

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