Dear Mark and Justin,<div><br></div><div>Thanks for your help, as a beginner to GROMACS i think i have to spend even more time with each option and make sure i know what i am doing. I will spend some time by using different electrostatic options with out pbc and let you know what happens to the simulations.</div>
<div><br></div><div>Thanks</div><div>Srinivas.<br><br><div class="gmail_quote">On Fri, Apr 9, 2010 at 1:26 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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 9/04/2010 1:25 PM, jampani srinivas wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Justin,<br>
<br><div><div></div><div class="h5">
I am sorry for the poor description of the problem, OK let me explain<br>
you clearly here.<br>
<br>
I have taken a decapeptide and solvated it with box size 6.0 nm, I want<br>
to create a frozen wall (confined sphere) around protein after a certain<br>
radius (in this case it is 2.5 nm). To achieve this i made two<br>
temperature coupling groups, first (Tmp1) one has protein and waters<br>
within 2.5nm from the center of the box and rest is second temperature<br>
coupling group (Tmp2). Initially when i run the simulation it was<br>
creating nrdf = 0 for both groups, Berk has helped me with a file<br>
readir.c file, i compiled my gromacs again that problem was solved. I<br>
have submitted simulations again and found that the energy was blowing<br>
up. I think you know the story after this. Earlier I want protein to<br>
interact with inner wall of the frozen group and check what happens,<br>
because of this I have never looked at the energygrps_excl option. I<br>
have done with both 2 and 4 fs time steps and I took 4fs option to speed<br>
up the simulation, and I have to still look at the paper you suggested me.<br>
<br>
Thanks for your suggestions, I have implemented your suggestion one<br>
after the other, finally when i use the energygrps_excl option it worked<br>
out. Now there is no sudden drift in the energy, and also i checked the<br>
velocities of non-frozen group is mostly zero (except for first frame)<br>
<br>
When I use the energygrps_excel option in the following way i am getting<br>
the below mentioned note i have to still understand what is this<br>
message. On the other hand if i use only "energygrp_excl = Tmp2 Tmp2<br>
Tmp2 Tmp1" line in mdp file i am getting fatal error. Is it necessary<br>
to to define the energy groups first and later exclude the energy option?<br>
</div></div></blockquote>
<br>
Yes, energy group exclusions require matching energy group definitions. The relevant part of manual 7.3 probably says this.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
+++++++++++++++++++++++++++++<br>
<br>
energygrps = Tmp1 Tmp2<br>
energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1<br>
<br>
++++++++++++++++++++++++++++++++<br>
<br>
NOTE<br>
<br>
"Can not exclude the lattice Coulomb energy between energy groups"<br>
</blockquote>
<br></div>
You seem to be trying to simulate a droplet inside a rigid shell of water. If so, why do you want the system to be periodic? You don't want periodicity artefacts *and* frozen-water-shell artefacts. There are other electrostatics models better suited than PME to such situations. You should look in the literature for successful published methodologies, rather than risk inventing a square wheel yourself before you've got enough experience to be confident with what you're doing.<br>
<br>
Here, the reciprocal-space part of the PME calculation must contain contributions from your excluded energy-groups, so you've got some Frankenstein possible worst-of-all-worlds combination. If I got such a paper to review, I'd need to see some serious groundwork justifying such a choice.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I used -maxwarn option here and generated the tpr file. I hope this does<br>
not harm the simulation.<br>
</blockquote>
<br></div>
That's a risky strategy. The programmer didn't put in such a message just to see whether he could do it...<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>*********************************************<br>J. Srinivasa Rao <br>Post-doctoral Research Associate<br>C/o Prof. Luis R Cruz Cruz<br>Computational Biophysics Group<br>
Department of Physics<br>Drexel University<br>3141 Chestnut St<br>Philadelphia, PA 19104, USA.<br>Ph: Off: 215-895-1989<br> Mob: 704-706-4191<br>Web:<a href="http://jsrao.web.officelive.com/default.aspx">http://jsrao.web.officelive.com/default.aspx</a><br>
**********************************************<br><br><br>
</div>