[gmx-users] grompp_d and mdrun_d issues with GBSA and normal mode analysis

[Ehud Schreiber]

Dear GROMACS users,

 

I am encountering a couple of issues when trying to perform normal mode
analysis in an implicit solvent (GBSA) setting.

I am using version 4.5.1 with double precision; unfortunately I do not
have the single precision version installed for comparison.

 

The starting point is a small protein which was energy minimized in two
stages, also in double precision and with GBSA, producing "em2" files.
The mdp file used for the normal mode analysis is the following:

 

----------------- nm.mdp -------------------------

integrator       = nm

nsteps           = 1

implicit_solvent = GBSA

gb_algorithm     = Still ; the default

rgbradii         = 1.0 ; must be equal to rlist 

rlist            = 1.0

coulombtype      = cut-off 

rcoulomb         = 1.0

vdwtype          = cut-off

rvdw             = 1.0

-------------------------------------------------------  

 

The command used is 

 

grompp_d -f nm.mdp -p topol.top -c em2.gro -t em2.trr -o nm.tpr

 

which ran fine except for the following note:

 

NOTE 1 [file nm.mdp]:

  You are using a plain Coulomb cut-off, which might produce artifacts.

  You might want to consider using PME electrostatics.

 

Then, I tried to run

 

mdrun_d -v -nice 0 -deffnm nm

 

However, the command seems to be stuck, and the following serious
warning is produced:

 

Warning: 1-4 interaction between 64 and 71 at distance 3.114 which is
larger than the 1-4 table size 2.000 nm

These are ignored for the rest of the simulation

This usually means your system is exploding,

if not, you should increase table-extension in your mdp file

or with user tables increase the table size

Maximum force: 3.48709e+06

Maximum force probably not small enough to ensure that you are in an 

energy well. Be aware that negative eigenvalues may occur when the

resulting matrix is diagonalized.

 

The em2.gro is definitely not having such a large distance between atoms
64 and 71:

 

    6GLN     CB   64   1.879   1.895   2.423

.

.

    6GLN    OE1   71   2.047   1.715   2.642

 

which are only about 0.346 nm apart. Also, the energy minimization,
which used the same options, mutatis mutandis,

 

---------------------- em2.mdp ----------------------------------

integrator       = cg

nsteps           = 1000

nstcgsteep       = 40 

implicit_solvent = GBSA

gb_algorithm     = Still ; the default

rgbradii         = 1.0 ; must be equal to rlist 

nstlist          = 10

rlist            = 1.0

coulombtype      = cut-off

rcoulomb         = 1.0

vdwtype          = cut-off

rvdw             = 1.0

nstenergy        = 10

---------------------------------------------------------------------

 

converged to machine precision having a much smaller maximum force:

 

Stepsize too small, or no change in energy.

Converged to machine precision,

but not to the requested precision Fmax < 10

 

Polak-Ribiere Conjugate Gradients converged to machine precision in 0
steps,

but did not reach the requested Fmax < 10.

Potential Energy  = -2.71868395521758e+04

Maximum force     =  4.63436548427712e+02 on atom 584

Norm of force     =  1.25296847735530e+02

 

The other problem arises when I try to follow the grompp_d note above
and change in nm.mdp to

 

coulombtype      = pme

 

I then have a fatal error:

 

ERROR 1 [file nm.mdp]:

  With GBSA, coulombtype must be equal to Cut-off

 

Am I doing something wrong or are there still some problems in the new
GBSA option of version 4.5.1?

 

Thanks,

Ehud Schreiber.

  

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