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<p class=MsoNormal>Dear GROMACS users,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I am encountering a couple of issues when trying to perform
normal mode analysis in an implicit solvent (GBSA) setting.<o:p></o:p></p>
<p class=MsoNormal>I am using version 4.5.1 with double precision;
unfortunately I do not have the single precision version installed for comparison.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>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:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>----------------- nm.mdp -------------------------<o:p></o:p></p>
<p class=MsoNormal>integrator = nm<o:p></o:p></p>
<p class=MsoNormal>nsteps
= 1<o:p></o:p></p>
<p class=MsoNormal>implicit_solvent = GBSA<o:p></o:p></p>
<p class=MsoNormal>gb_algorithm = Still ; the default<o:p></o:p></p>
<p class=MsoNormal>rgbradii =
1.0 ; must be equal to rlist <o:p></o:p></p>
<p class=MsoNormal>rlist
= 1.0<o:p></o:p></p>
<p class=MsoNormal>coulombtype = cut-off <o:p></o:p></p>
<p class=MsoNormal>rcoulomb =
1.0<o:p></o:p></p>
<p class=MsoNormal>vdwtype
= cut-off<o:p></o:p></p>
<p class=MsoNormal>rvdw
= 1.0<o:p></o:p></p>
<p class=MsoNormal>------------------------------------------------------- <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>The command used is <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>grompp_d -f nm.mdp -p topol.top -c em2.gro -t em2.trr -o
nm.tpr<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>which ran fine except for the following note:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>NOTE 1 [file nm.mdp]:<o:p></o:p></p>
<p class=MsoNormal> You are using a plain Coulomb cut-off, which might
produce artifacts.<o:p></o:p></p>
<p class=MsoNormal> You might want to consider using PME electrostatics.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Then, I tried to run<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>mdrun_d -v -nice 0 -deffnm nm<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>However, the command seems to be stuck, and the following
serious warning is produced:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Warning: 1-4 interaction between 64 and 71 at distance 3.114
which is larger than the 1-4 table size 2.000 nm<o:p></o:p></p>
<p class=MsoNormal>These are ignored for the rest of the simulation<o:p></o:p></p>
<p class=MsoNormal>This usually means your system is exploding,<o:p></o:p></p>
<p class=MsoNormal>if not, you should increase table-extension in your mdp file<o:p></o:p></p>
<p class=MsoNormal>or with user tables increase the table size<o:p></o:p></p>
<p class=MsoNormal>Maximum force: 3.48709e+06<o:p></o:p></p>
<p class=MsoNormal>Maximum force probably not small enough to ensure that you
are in an <o:p></o:p></p>
<p class=MsoNormal>energy well. Be aware that negative eigenvalues may occur
when the<o:p></o:p></p>
<p class=MsoNormal>resulting matrix is diagonalized.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>The em2.gro is definitely not having such a large distance
between atoms 64 and 71:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal> 6GLN
CB 64 1.879 1.895 2.423<o:p></o:p></p>
<p class=MsoNormal>.<o:p></o:p></p>
<p class=MsoNormal>.<o:p></o:p></p>
<p class=MsoNormal> 6GLN OE1
71 2.047 1.715 2.642<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>which are only about 0.346 nm apart. Also, the energy
minimization, which used the same options, mutatis mutandis,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>---------------------- em2.mdp
----------------------------------<o:p></o:p></p>
<p class=MsoNormal>integrator = cg<o:p></o:p></p>
<p class=MsoNormal>nsteps
= 1000<o:p></o:p></p>
<p class=MsoNormal>nstcgsteep = 40 <o:p></o:p></p>
<p class=MsoNormal>implicit_solvent = GBSA<o:p></o:p></p>
<p class=MsoNormal>gb_algorithm = Still ; the default<o:p></o:p></p>
<p class=MsoNormal>rgbradii =
1.0 ; must be equal to rlist <o:p></o:p></p>
<p class=MsoNormal>nstlist
= 10<o:p></o:p></p>
<p class=MsoNormal>rlist
= 1.0<o:p></o:p></p>
<p class=MsoNormal>coulombtype = cut-off<o:p></o:p></p>
<p class=MsoNormal>rcoulomb =
1.0<o:p></o:p></p>
<p class=MsoNormal>vdwtype
= cut-off<o:p></o:p></p>
<p class=MsoNormal>rvdw
= 1.0<o:p></o:p></p>
<p class=MsoNormal>nstenergy = 10<o:p></o:p></p>
<p class=MsoNormal>---------------------------------------------------------------------<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>converged to machine precision having a much smaller maximum
force:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Stepsize too small, or no change in energy.<o:p></o:p></p>
<p class=MsoNormal>Converged to machine precision,<o:p></o:p></p>
<p class=MsoNormal>but not to the requested precision Fmax < 10<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Polak-Ribiere Conjugate Gradients converged to machine
precision in 0 steps,<o:p></o:p></p>
<p class=MsoNormal>but did not reach the requested Fmax < 10.<o:p></o:p></p>
<p class=MsoNormal>Potential Energy = -2.71868395521758e+04<o:p></o:p></p>
<p class=MsoNormal>Maximum force =
4.63436548427712e+02 on atom 584<o:p></o:p></p>
<p class=MsoNormal>Norm of force =
1.25296847735530e+02<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>The other problem arises when I try to follow the grompp_d note
above and change in nm.mdp to<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>coulombtype = pme<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I then have a fatal error:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>ERROR 1 [file nm.mdp]:<o:p></o:p></p>
<p class=MsoNormal> With GBSA, coulombtype must be equal to Cut-off<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Am I doing something wrong or are there still some problems
in the new GBSA option of version 4.5.1?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks,<o:p></o:p></p>
<p class=MsoNormal>Ehud Schreiber.<o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
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