Hi,
For the moment you can add the option -nt 1 to mdrun, which will make it run
without problems.
Berk
From: per.lars...@sbc.su.se
Subject: Re: [gmx-users] grompp_d and mdrun_d issues with GBSA and normal mode
analysis
Date: Tue, 7 Sep 2010 16:12:28 +0200
To: gmx-users@gromacs.org
This has been fixed with Berk's commit c06ee471...The error was not related to
GB, but rather a combination of domain decomp.+nm+cut-offs.
Cheers/Per
6 sep 2010 kl. 11.38 skrev 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 = nmnsteps =
1implicit_solvent = GBSAgb_algorithm = Still ; the defaultrgbradii
= 1.0 ; must be equal to rlistrlist = 1.0coulombtype =
cut-offrcoulomb = 1.0vdwtype = cut-offrvdw =
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 nmThese are ignored for the
rest of the simulationThis usually means your system is exploding,if not, you
should increase table-extension in your mdp fileor with user tables increase
the table sizeMaximum force: 3.48709e+06Maximum force probably not small enough
to ensure that you are in anenergy well. Be aware that negative eigenvalues may
occur when theresulting 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 = cgnsteps =
1000nstcgsteep = 40implicit_solvent = GBSAgb_algorithm = Still ; the
defaultrgbradii = 1.0 ; must be equal to rlistnstlist =
10rlist = 1.0coulombtype = cut-offrcoulomb = 1.0vdwtype
= cut-offrvdw = 1.0nstenergy =
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+04Maximum force =
4.63436548427712e+02 on atom 584Norm 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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