Bug #1065

Error with MARTINI depending by the box size

Added by Francesco Oteri about 7 years ago. Updated about 7 years ago.

preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
Affected version:


Dear gromacs users,
I am facing a very tricky problem in building a stable topology.
In particular I am trying to use MARTINI force-field and I noticed that:
if I use a box whose the side size is smaller than 20nm, the minimization fails with this message:

Reading file 01em.tpr, VERSION 4.6-beta1 (single precision)
Starting 12 tMPI threads
Using 12 MPI threads
Making 2D domain decomposition 4 x 3 x 1

Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 2000
Step= 14, Dmax= 1.2e-06 nm, Epot= 4.42099e+18 Fmax= inf, atom= 39063
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 1000 (whichmay not be possible for your system).
It stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.
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 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 4.4209897e+18
Maximum force = inf on atom 39063
Norm of force = inf

gcq#142: "One Ripple At a Time" (Bianca's Smut Shack)

But, if I use a box bigger then 19.5nm the minimization, although with some LINCS warning, succeeded!

I found the problem with either gromacs 4.5.5 or 4.6beta1.

I am attaching the script (crea_topo.csh) I am using to build the topologies and all the input files
you need to replicate the error
The different topologies have been obtained changing the value of the variable side inside crea_topo.csh

Can you give me some clue on how to solve the problem, except changing the software?.
I mean, I would like to know whether there is a bug or not in some of the program used to build the topology.

water-1bar-303K.gro (728 KB) water-1bar-303K.gro water box with MARTINI force-field Francesco Oteri, 12/10/2012 06:05 PM (267 KB) script to build the MARTINI topology Francesco Oteri, 12/10/2012 06:05 PM
martini.itp (49.7 KB) martini.itp MARTINI 2.2 atomtype definition Francesco Oteri, 12/10/2012 06:05 PM
ions.itp (1.18 KB) ions.itp MARTINI 2.2 atomtype definition for ions Francesco Oteri, 12/10/2012 06:05 PM
dsspcmbi (47.6 KB) dsspcmbi dssp executable Francesco Oteri, 12/10/2012 06:05 PM
Desu_OK.pdb (941 KB) Desu_OK.pdb Input PDB Francesco Oteri, 12/10/2012 06:05 PM
01em.mdp (2.51 KB) 01em.mdp Input file for the minimization Francesco Oteri, 12/10/2012 06:05 PM
crea_topo.csh (1.02 KB) crea_topo.csh Scrip used to produce the topology Francesco Oteri, 12/10/2012 06:05 PM
crea_topo.csh (1.3 KB) crea_topo.csh Francesco Oteri, 12/10/2012 07:42 PM


#1 Updated by Justin Lemkul about 7 years ago

  • Category changed from build system to preprocessing (pdb2gmx,grompp)
  • Status changed from New to Feedback wanted
  • Priority changed from Normal to Low

I don't think there is sufficient evidence to call this a bug. It seems to me that there is simply an issue with the construction of the system. Note that you should never get LINCS warnings in a stable EM process, so there doesn't seem to be a big difference in your results. You note complete failure with a box < 20 nm, but the instability persists even when increasing the box size. The only thing that might depend on the box size is the way in which the solvent is placed within the box, so you probably just have some inconvenient overlap with solvent particles. The output from mdrun tells you which atom has the biggest problem; it should be straightforward to identify the source of the atomic overlap or bad geometry.

#2 Updated by Francesco Oteri about 7 years ago

Now I updated the script crea_topo in order to:
1)minimize the protein in vacuo
2)water molecules closer then 0.8 nm from the protein are deleted from the file created by genbox

These operations result in the absence of any LINCS warning and, hence, a correct EM when a box side is
at least 20nm. Again I obtain the same error when the box is 19nm.

#3 Updated by Roland Schulz about 7 years ago

  • Status changed from Feedback wanted to Closed

Have you identified the atoms as Justin has suggested. Please use the gmx-users mailing list to get help on how to debug your system. Closing for now with the assumption that it is a setup problem. After you have ruled out (with the help of others from the mailing-list) that this isn't a system setup problem (and might be a bug), it can be reopened.

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