<br><br><div class="gmail_quote">On Fri, Apr 3, 2009 at 9:48 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;">
Manik Mayur wrote:<div><div class="h5"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>> wrote:<br>
<br>
Manik Mayur wrote:<br>
<br>
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<br>
couette flow using GROMACS. If yes, then please suggest what<br>
specific steps has to be taken. If no, then are the developers<br>
planning to implement giving constant velocity to a group of<br>
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<br>
problems.<br>
<br>
<br>
As the mail you pointed to suggest, it is quite simple to do<br>
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<br>
in the input file (mdp) you enter the velocity instead of the<br>
acceleration in the appropriate entries, and you are good to go. You<br>
may need to remove the mean velocity of the group as well...<br>
<br>
<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>
</blockquote></div></div>
You didn't mention that :(.<br>
No, you will have to do some more hacking, but you could e.g. make group 0 to have acceleration and group 1 a velocity.<br>
</blockquote><br>Can you provide more insight on how to achieve it, as from your suggestion it turns out, I can have either constant velocity build of GROMACS or the constant acceleration one.<br><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<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">
<br>
<br>
<br>
Also can we build GROMACS as a library to be called from<br>
customized codes?<br>
<br>
Thanks,<br>
-- Manik Mayur<br>
Graduate student<br>
Microfluidics Lab<br>
Dept. of Mechanical Engg.<br>
IIT Kharagpur<br>
INDIA<br>
<br>
<br>
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<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></div>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<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> <mailto:<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><div class="im">
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<br>
<br>
<br>
<br>
-- <br>
Manik Mayur<br>
Graduate student<br>
Microfluidics Lab<br>
Dept. of Mechanical Engg.<br>
IIT Kharagpur<br>
INDIA<br>
<br>
<br>
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</div></blockquote><div><div></div><div class="h5">
<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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</div></div></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>