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Bug #548

grompp_d and mdrun_d issues with GBSA and normal mode analysis

Added by Ehud Schreiber about 9 years ago. Updated about 9 years ago.

Status:
Closed
Priority:
Normal
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Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
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Description

Dear GROMACS developers,

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.

bugzilla.tar (170 KB) bugzilla.tar tar file of nm.mdp topol.top em2.gro em2.trr Ehud Schreiber, 09/06/2010 04:39 PM
bugzilla2.tar (690 KB) bugzilla2.tar tar file of topol_A.itp topol_B.itp topol_C.itp topol_P.itp Ehud Schreiber, 09/07/2010 10:05 AM

History

#1 Updated by Ehud Schreiber about 9 years ago

Created an attachment (id=532)
tar file of nm.mdp topol.top em2.gro em2.trr

#2 Updated by Per Larsson about 9 years ago

Hi!

Could you also upload the itp-files for your A,B,C, and P chains (included from topol.top)

Thanks
/Per

(In reply to comment #1)

Created an attachment (id=532) [details]
tar file of nm.mdp topol.top em2.gro em2.trr

#3 Updated by Ehud Schreiber about 9 years ago

Created an attachment (id=533)
tar file of topol_A.itp topol_B.itp topol_C.itp topol_P.itp

the paths of these included itp files will probably need to be changed in topol.top

#4 Updated by Per Larsson about 9 years ago

Hi

In the end, this was not a GB-issue, but rather a combination of domain decomp.+nm+cutoffs.
It is fixed now by commit c06ee471448f38311028d1bcc17066d3f4f1c1b9

/Per

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