Thanks for the quick feedback!<br><br>
<div><span class="gmail_quote">On 5/10/06, <b class="gmail_sendername">Erik Lindahl</b> <<a href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br><br>On May 10, 2006, at 1:24 PM, David van der Spoel wrote:<br><br>> Viswanadham Sridhara wrote:
<br>>> Hi everyone,<br>>> This is regarding implementation of time-dependent electric field<br>>> on the system.<br>>> I tried looking into the manual, and did a bit of survey in<br>>> mailing lists. I still dont know how to implement E_zt in .mdp
<br>>> options.<br>>> As an example, can anyone tell me how to implement a 5ns E (V/nm)<br>>> trapezoidal pulse (1ns rise and fall times with 3ns pulse on time).<br>> you can't.<br>><br>> please check the source code, src/mdlib/sim_util.c
<br><br>To clarify - the routine in question is called calc_f_el() and is<br>_extremely_ simple, so you can probably implement it yourself with<br>very little extra work.<br><br>The coordinates of particule i (counting starts from 0, since we're
<br>using C) are available in units of nm in<br><br>x[i][XX]<br>x[i][YY]<br>x[i][ZZ]<br><br>Similarly, the forces you want to alter are in units of kJ/mol/nm, in<br><br>f[i][XX]<br>f[i][YY]<br>f[i][ZZ]<br><br>... and the particle charge is charge[i], in electron charge units.
<br><br>So, go through all particles, check e.g. the z-coordinate and assign<br>a field in V/nm based on this. We need to convert it to MD units too,<br>so the force correction will be<br><br>f[i][ZZ] += your_calculated_field_at_this_z_coordiate * FIELDFAC *
<br>charge[i].<br><br><br><br>Cheers,<br><br>Erik<br><br><br><br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Graduate Research Assistant,
<br>Old Dominion University,<br>Norfolk, VA-23529.