<br><br><div class="gmail_quote">On Fri, Apr 3, 2009 at 8:25 PM, 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">Manik Mayur wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
With reference to<br>
<br>
<a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html" target="_blank">http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html</a><br>
<br>
I would like to know if anybody has successfully simulated couette flow using GROMACS. If yes, then please suggest what specific steps has to be taken. If no, then are the developers planning to implement giving constant velocity to a group of atoms, as we can do in LAMMPS, in future versions.<br>
<br>
It will really be a life saver if GROMACS can be used for such problems. <br>
</blockquote>
<br></div>
As the mail you pointed to suggest, it is quite simple to do yourself. As a first guess look for routine<br>
static void do_update_md(int start,int homenr,double dt,<br>
<br>
in src/mdlib/update.c<br>
<br>
and find this line:<br>
<br>
/* do not scale the mean velocities u */<br>
vn = gstat[ga].u[d] + accel[ga][d]*dt + vnrel;<br>
<br>
and replace it by<br>
<br>
/* do not scale the mean velocities u */<br>
vn = gstat[ga].u[d] + accel[ga][d] + vnrel;<br>
<br>
and recompile.<br>
<br>
As you see, I just removed the multiplication by the time step. Now in the input file (mdp) you enter the velocity instead of the acceleration in the appropriate entries, and you are good to go. You may need to remove the mean velocity of the group as well...</blockquote>
<div><br>Thanks a lot for the suggestion. But will this work if I have 2 groups, one with constant velocity and another with constant acceleration? Like a superposition of couette and poiseuille flow.<br> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Also can we build GROMACS as a library to be called from customized codes?<br>
<br>
Thanks,<br>
-- <br>
Manik Mayur<br>
Graduate student<br>
Microfluidics Lab<br>
Dept. of Mechanical Engg.<br>
IIT Kharagpur<br>
INDIA<br>
<br>
<br></div>
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</blockquote>
<br>
<br>
-- <br>
David.<br>
________________________________________________________________________<br>
David van der Spoel, PhD, Professor of Biology<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: 46 18 471 4205 fax: 46 18 511 755<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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</blockquote></div><br><br clear="all"><br>-- <br>Manik Mayur<br>Graduate student<br>Microfluidics Lab<br>Dept. of Mechanical Engg.<br>IIT Kharagpur<br>INDIA<br>