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

[Berk Hess]

Hi,

For the moment you can add the option -nt 1 to mdrun, which will make it run without problems.

Berk

From: per.larsson at 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 at 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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