<br><br><div class="gmail_quote">On Fri, Apr 3, 2009 at 11:11 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:<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>
On Fri, Apr 3, 2009 at 10:47 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>
<br>
<br>
On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel<br>
<<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>><br></div><div><div class="h5">
<mailto:<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>
<br>
<br>
On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel<br>
<<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>><br>
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<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<br>
simulated<br>
couette flow using GROMACS. If yes, then please<br>
suggest what<br>
specific steps has to be taken. If no, then are the<br>
developers<br>
planning to implement giving constant velocity to<br>
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<br>
used for<br>
such<br>
problems.<br>
<br>
<br>
As the mail you pointed to suggest, it is quite simple<br>
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] +<br>
accel[ga][d]*dt +<br>
vnrel;<br>
<br>
and replace it by<br>
<br>
/* do not scale the mean velocities u */<br>
vn = gstat[ga].u[d] +<br>
accel[ga][d] + vnrel;<br>
<br>
and recompile.<br>
<br>
As you see, I just removed the multiplication by the time<br>
step. Now<br>
in the input file (mdp) you enter the velocity instead<br>
of the<br>
acceleration in the appropriate entries, and you are<br>
good to<br>
go. You<br>
may need to remove the mean velocity of the group as<br>
well...<br>
<br>
<br>
Thanks a lot for the suggestion. But will this work if I<br>
have 2<br>
groups, one with constant velocity and another with constant<br>
acceleration? Like a superposition of couette and<br>
poiseuille flow.<br>
<br>
You didn't mention that :(.<br>
No, you will have to do some more hacking, but you could e.g.<br>
make<br>
group 0 to have acceleration and group 1 a velocity.<br>
<br>
<br>
Can you provide more insight on how to achieve it, as from your<br>
suggestion it turns out, I can have either constant velocity<br>
build of GROMACS or the constant acceleration one.<br>
<br>
if (g == 0)<br>
APPLy acceleration<br>
else if (g == 1)<br>
apply velocity<br>
else<br>
do normal update<br>
<br>
I really appreciate your help. One last doubt, what is this 'g' or the group you are talking about? As we define acc_grps by their names and not numbers in the mdp file. Do we have to introduce some new parameter 'g' which will be defined as 0 or 1 accordingly?<br>
</div></div></blockquote>
EasY:<br>
<br>
acc_groups = Cucumber TOmata<br>
means Cucumber = 0, Tomato = 1<div class="im"><br>
</div></blockquote><div class="im"><br>Got it. :) Thanks a lot.<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;"><div class="im"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Also, can't we have this feature in the main stream GROMACS rather than having our own custom build, something like vel_grps? Just a suggestion.<br>
</blockquote></div>
Sure, but that doesn't help you now.<br>
</blockquote><br>Yes, but I would like to see my favorite MD package as one of the most versatile package available :)<br><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5">
<br>
Thanks,<br>
<br>
<br>
<br>
Also can we build GROMACS as a library to be<br>
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 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>
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IIT Kharagpur<br>
INDIA<br>
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________________________________________________________________________<br>
David van der Spoel, PhD, Professor of Biology<br>
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Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
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________________________________________________________________________<br>
David van der Spoel, PhD, Professor of Biology<br>
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phone: 46 18 471 4205 fax: 46 18 511 755<br>
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<br>
-- <br>
Manik Mayur<br>
Graduate student<br>
Microfluidics Lab<br>
Dept. of Mechanical Engg.<br>
IIT Kharagpur<br>
INDIA<br>
<br>
<br>
------------------------------------------------------------------------<br>
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</div></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>