<li><a HREF="#shellmd"><b>shell molecular dynamics</b></a>(emtol,niter,fcstep)
<li><a HREF="#tpi"><b>test particle insertion</b></a>(rtpi)
<li><A HREF="#out"><b>output control</b></A> (nstxout, nstvout, nstfout, nstlog, nstcalcenergy, nstenergy, nstxtcout, xtc-precision, xtc-grps, energygrps)
-<li><A HREF="#nl"><b>neighbor searching</b></A> (cutoff-scheme, nstlist, nstcalclr, ns-type, pbc, periodic-molecules, verlet-buffer-drift, rlist, rlistlong)
+<li><A HREF="#nl"><b>neighbor searching</b></A> (cutoff-scheme, nstlist, nstcalclr, ns-type, pbc, periodic-molecules, verlet-buffer-tolerance, rlist, rlistlong)
<li><A HREF="#el"><b>electrostatics</b></A> (coulombtype, coulomb-modifier, rcoulomb-switch, rcoulomb, epsilon-r, epsilon-rf)
<li><A HREF="#vdw"><b>VdW</b></A> (vdwtype, vdw-modifier, rvdw-switch, rvdw, DispCorr)
<li><A HREF="#table"><b>tables</b></A> (table-extension, energygrp-table)
<dt><b>Verlet</b></dt>
<dd>Generate a pair list with buffering. The buffer size is automatically set
-based on <b>verlet-buffer-drift</b>, unless this is set to -1, in which case
+based on <b>verlet-buffer-tolerance</b>, unless this is set to -1, in which case
<b>rlist</b> will be used. This option has an explicit, exact cut-off at
<b>rvdw</b>=<b>rcoulomb</b>. Currently only cut-off, reaction-field,
PME electrostatics and plain LJ are supported. Some <tt>mdrun</tt> functionality
the neighbor list is made only once.
With energy minimization the neighborlist will be updated for every
energy evaluation when <b>nstlist</b><tt>>0</tt>.
-With non-bonded force calculation on the GPU, a value of 20 or more gives
-the best performance.</dd>
+With <b>cutoff-scheme=Verlet</b> and <b>verlet-buffer-tolerance</b> set,
+<b>nstlist</b> is actually a minimum value and <tt>mdrun</tt> might increase it.
+With parallel simulations and/or non-bonded force calculation on the GPU,
+a value of 20 or 40 often gives the best performance.
+With <b>cutoff-scheme=Group</b> and non-exact cut-off's, <b>nstlist</b> will
+affect the accuracy of your simulation and it can not be chosen freely.
+</dd>
<dt><b>0</b></dt>
<dd>The neighbor list is only constructed once and never updated.
This is mainly useful for vacuum simulations in which all particles
and molecules are not made whole in the output</dd>
</dl></dd>
-<dt><b>verlet-buffer-drift: (0.005) [kJ/mol/ps]</b></dt>
-<dd>Useful only with <b>cutoff-scheme</b>=<b>Verlet</b>. This sets the target energy drift
-per particle caused by the Verlet buffer, which indirectly sets <b>rlist</b>.
+<dt><b>verlet-buffer-tolerance: (0.005) [kJ/mol/ps]</b></dt>
+<dd>Useful only with <b>cutoff-scheme</b>=<b>Verlet</b>. This sets the maximum
+allowed error for pair interactions per particle caused by the Verlet buffer,
+which indirectly sets <b>rlist</b>.
As both <b>nstlist</b> and the Verlet buffer size are fixed
(for performance reasons), particle pairs not in the pair list can occasionally
get within the cut-off distance during <b>nstlist</b>-1 nsteps. This
-generates energy drift. In a constant-temperature ensemble, the drift can be
+causes very small jumps in the energy. In a constant-temperature ensemble,
+these very small energy jumps can be
estimated for a given cut-off and <b>rlist</b>. The estimate assumes a
-homogeneous particle distribution, hence the drift might be slightly
+homogeneous particle distribution, hence the errors might be slightly
underestimated for multi-phase systems. For longer pair-list life-time
-(<b>nstlist</b>-1)*dt the drift is overestimated, because the interactions
+(<b>nstlist</b>-1)*dt the buffer is overestimated, because the interactions
between particles are ignored. Combined with cancellation of errors,
-the actual energy drift is usually one to two orders of magnitude smaller.
+the actual drift of the total energy is usually one to two orders of magnitude
+smaller.
Note that the generated buffer size takes into account that
the GROMACS pair-list setup leads to a reduction in the drift by
a factor 10, compared to a simple particle-pair based list.
Without dynamics (energy minimization etc.), the buffer is 5% of the cut-off.
For dynamics without temperature coupling or to override the buffer size,
-use <b>verlet-buffer-drift</b>=-1 and set <b>rlist</b> manually.</dd>
+use <b>verlet-buffer-tolerance</b>=-1 and set <b>rlist</b> manually.</dd>
<dt><b>rlist: (1) [nm]</b></dt>
<dd>Cut-off distance for the short-range neighbor list.
With <b>cutoff-scheme</b>=<b>Verlet</b>, this is by default set by the
-<b>verlet-buffer-drift</b> option and the value of <b>rlist</b> is ignored.</dd>
+<b>verlet-buffer-tolerance</b> option and the value of <b>rlist</b> is ignored.</dd>
<dt><b>rlistlong: (-1) [nm]</b></dt>
<dd>Cut-off distance for the long-range neighbor list.
<A HREF="#user">userreal4</A><br>
<A HREF="#vdw">vdwtype</A><br>
<A HREF="#vdw">vdw-modifier</A><br>
-<A HREF="#nl">verlet-buffer-drift</A><br>
+<A HREF="#nl">verlet-buffer-tolerance</A><br>
<A HREF="#out">xtc-grps</A><br>
<A HREF="#out">xtc-precision</A><br>
<A HREF="#sa">zero-temp-time</A><br>
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff