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<DIV><FONT face=Arial size=2>I am trying to simulate stearic acid in a crystal
form. My simulation box is a multiple of the unitcell of the crystal and I
have 6 copies of the unitcell in each direction. After I run a NPT
simulation at a temperature (300K) the crystal is stable (below the melting
temperature) but I have more movement in the individual stearic acids then I
would expect. While they are remaining ordered, the acid group and
portions of the alkane tail are rotating so that there is a lot of variability
between stearic acids. This rotating is so much I'm seeing a small
shift in the layer spacing in one direction. I am using all-bonds constraints
using LINCS and comm_mode = angular. From the manual it appeared to me
that there were corrections to the energy so that the lack of bond vibration is
accounted for in the temperature but I wasn't completely sure. Could the
all-bonds LINCS constraint cause more energy to be in bond rotations, would
problems with my box (not big enough, etc.) be more likely, or could it be
something else?</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Below is my .mdp file</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thanks</FONT></DIV>
<DIV><FONT face=Arial size=2>Andrea</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT size=1>
<P><FONT face=Arial size=2>title = Stearic acid polymorph C </FONT></P>
<P><FONT face=Arial size=2>cpp = /lib/cpp</FONT></P>
<P><FONT face=Arial size=2>include = -I../top</FONT></P>
<P><FONT face=Arial size=2>integrator = md</FONT></P>
<P><FONT face=Arial size=2>comm-grps = Str </FONT></P>
<P><FONT face=Arial size=2>nstcomm = 1</FONT></P>
<P><FONT face=Arial size=2>comm-mode = angular</FONT></P>
<P><FONT face=Arial size=2>dt = 0.002</FONT></P>
<P><FONT face=Arial size=2>nsteps = 500000</FONT></P>
<P><FONT face=Arial size=2>nstxout = 500000</FONT></P>
<P><FONT face=Arial size=2>nstvout = 500000</FONT></P>
<P><FONT face=Arial size=2>nstlog = 1000</FONT></P>
<P><FONT face=Arial size=2>nstenergy = 1000</FONT></P>
<P><FONT face=Arial size=2>nstxtcout = 1000</FONT></P>
<P><FONT face=Arial size=2>xtc_grps = Str </FONT></P>
<P><FONT face=Arial size=2>energygrps = Str </FONT></P>
<P><FONT face=Arial size=2>nstlist = 5</FONT></P>
<P><FONT face=Arial size=2>ns_type = grid</FONT></P>
<P><FONT face=Arial size=2>pbc = xyz</FONT></P>
<P><FONT face=Arial size=2>;PME protocol: Check it!</FONT></P>
<P><FONT face=Arial size=2>;coulombtype = Reaction-field</FONT></P>
<P><FONT face=Arial size=2>;rlist = 0.9 </FONT></P>
<P><FONT face=Arial size=2>;rcoulomb = 1.4</FONT></P>
<P><FONT face=Arial size=2>;rvdw = 1.0</FONT></P>
<P><FONT face=Arial size=2>;epsilon_r = 2</FONT></P>
<P><FONT face=Arial size=2>coulombtype = PME</FONT></P>
<P><FONT face=Arial size=2>rlist = 0.9 </FONT></P>
<P><FONT face=Arial size=2>rcoulomb = 0.9</FONT></P>
<P><FONT face=Arial size=2>rvdw = 0.9</FONT></P>
<P><FONT face=Arial size=2>fourierspacing = 0.12 </FONT></P>
<P><FONT face=Arial size=2>pme_order = 4 </FONT></P>
<P><FONT face=Arial size=2>ewald_rtol = 1e-5</FONT></P>
<P><FONT face=Arial size=2>optimize_fft = yes</FONT></P>
<P><FONT face=Arial size=2>;T- and P-coupling: Even if I use PME, just to be
safe</FONT></P>
<P><FONT face=Arial size=2>tcoupl = Berendsen </FONT></P>
<P><FONT face=Arial size=2>tc-grps = System</FONT></P>
<P><FONT face=Arial size=2>tau_t = 0.1 </FONT></P>
<P><FONT face=Arial size=2>ref_t = 300 </FONT></P>
<P><FONT face=Arial size=2>Pcoupl = Berendsen</FONT></P>
<P><FONT face=Arial size=2>pcoupltype = isotropic</FONT></P>
<P><FONT face=Arial size=2>tau_p = 1.0</FONT></P>
<P><FONT face=Arial size=2>compressibility = 5e-5</FONT></P>
<P><FONT face=Arial size=2>ref_p = 1.0</FONT></P>
<P><FONT face=Arial size=2>gen_vel = yes</FONT></P>
<P><FONT face=Arial size=2>gen_temp = 300</FONT></P>
<P><FONT face=Arial size=2>gen_seed = 503114 </FONT></P>
<P><FONT face=Arial size=2>constraints =
all-bonds</FONT></P></FONT></DIV></BODY></HTML>