Thanks David! That helped a lot. I'm now trying to use the walls feature with a user-defined potential. My mdp file is shown below: <div><br></div><div><div>title = Alkanethiol SAM MD</div><div>; Run parameters</div>
<div>integrator = md ; leap-frog integrator</div><div>nsteps = 500000 ; 2 * 500000 = 1000 ps, 1 ns</div><div>dt = 0.002 ; 2 fs</div><div>; Output control</div><div>nstxout = 1000 ; save coordinates every 2 ps</div>
<div>nstvout = 1000 ; save velocities every 2 ps</div><div>nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps</div><div>nstenergy = 1000 ; save energies every 2 ps</div>
<div>nstlog = 1000 ; update log file every 2 ps</div><div>energygrps = CH3 CH2 S wall0</div><div>energygrp_table = CH3 wall0 CH2 wall0 S wall0</div><div>; Bond parameters</div><div>continuation = yes ; Restarting after NPT</div>
<div>constraint_algorithm = lincs ; holonomic constraints</div><div>constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained</div><div>lincs_iter = 1 ; accuracy of LINCS</div><div>
lincs_order = 4 ; also related to accuracy</div><div>; Neighborsearching</div><div>ns_type = grid ; search neighboring grid cells</div><div>nstlist = 5 ; 10 fs</div><div>
rlist = 1.0 ; short-range neighborlist cutoff (in nm)</div><div>coulombtype = Cutoff</div><div>rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)</div><div>vdwtype = User</div>
<div>rvdw = 1.0 ; short-range van der Waals cutoff (in nm)</div><div>; Electrostatics</div><div>pme_order = 4 ; cubic interpolation</div></div><div><div>fourierspacing = 0.16 ; grid spacing for FFT</div>
<div>; Temperature coupling is on</div><div>tcoupl = V-rescale ; modified Berendsen thermostat</div><div>tc-grps = System ; two coupling groups - more accurate</div><div>tau_t = 0.1 ; time constant, in ps</div>
<div>ref_t = 300 ; reference temperature, one for each group, in K</div><div>; Pressure coupling is off</div><div>pcoupl = no ; Pressure coupling on in NPT</div><div>; Periodic boundary conditions</div>
<div>pbc = xy ; 3-D PBC</div><div>; Dispersion correction</div><div>DispCorr = no ; account for cut-off vdW scheme</div><div>; Walls</div><div>nwall = 1</div><div>wall_type = table</div>
<div>wall_atomtype = wall0</div><div>; Velocity generation</div><div>gen_vel = no ; Velocity generation is off</div></div><div><br></div><div>I've defined three energy groups in my system (CH3, CH2, and S), and I have built the following three energy group tables:</div>
<div> table_CH3_wall0.xvg</div><div> table_CH2_wall0.xvg</div><div> table_S_wall0.xvg</div><div>I'm not sure whether I should list wall0 among the [ atomtypes ]... When I do, grompp complains about wall0 not being found in the index file. I could add it, but since wall0 doesn't correspond to any actual atoms in my system, I'm not exactly sure how to proceed. </div>
<div><br></div><div>In summary, I'm confused as to how to combine the concepts of energy groups and walls when using potential tables.</div><div><br></div><div>Thank you so much!</div><div>Olivia</div><div> <br><br><div class="gmail_quote">
On Sat, Nov 26, 2011 at 10:13 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im">On 2011-11-26 15:58, Olivia Waring wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello all,<br>
<br>
I'm wondering if it's possible to use tables to simulate a z-dependent<br>
12-3 potential. I'd have the following function:<br>
<br>
V(z) = C12/(z-z0)^12 - C3/(z-z0)^3<br>
<br>
and I'm trying to construct a table to match. Any hints to get me<br>
started would be greatly appreciated.<br>
<br>
</blockquote></div>
If you mean z as just one cartesian coordinate you should look into the wall potential options.<br>
<br>
Otherwise you plot the function in tables as a function of z-z0, since it will be used with the distance. This is in the manual...<div class="HOEnZb"><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thank you!<br>
Olivia<br>
<br>
<br>
--<br>
Olivia Waring<br>
Princeton University '12<br>
AB Chemistry<br>
<br>
<br>
<br>
</blockquote>
<br>
<br></div></div><span class="HOEnZb"><font color="#888888">
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205" target="_blank">+46184714205</a>.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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