Dear Chris:<br><br>I don't think it is something related to pbc because my solutes are well<br>inside the simulation box (as I told you before I visualize them via a movie<br>while the simulation proceeds).<br><br>Nor it is something related to the barostat because I saw that warning<br>
and in order to try to see it work I decided to do NVT simulations.<br>However, the problem persists.<br><br>I'm using angle restraints on the "pulled" group in order to preserve its<br>orientation with respect to the reference group. Could this be the problem?<br>
<br>Cheers,<br><br> Giuseppe<br><br><div class="gmail_quote">2010/1/24 <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Giuseppe:<br>
<br>
OK, those are the forces. They seem pretty huge and massively fluctuating, although I use umbrella sampling myself so this might be quite normal for constraint sampling (something for you to look into).<br>
<br>
The only thing that comes to mind is that your running up against a pbc problem in determining either the center of mass of each protein prior to solving the constraint or that your constraint is oscillating about different "shortest distances" over different images.<br>
<br>
The gmx3 manual also says this:<br>
<br>
Another limitation is connected with pressure scaling. When pressure scaling is used, the shortest distance between the pull groups and the reference group should be within in the central unit-cell, not to periodic images of the pull groups. Otherwise the pressure scaling will affect the reference distances and thus also the forces. The exception is constraint pulling with constraint distance? > 0, this will work correctly with pressure scaling under all conditions.<br>
<br>
So here's what I recommend:<br>
<br>
1. create a system that has no water so that it runs faster.<br>
<br>
2. Use the sd integrator so that you get some random noise.<br>
integrator = sd<br>
tc_grps = System<br>
tau_t = 1.0<br>
ld_seed = -1<br>
ref_t = 300<br>
gen_temp = 300<br>
gen_vel = yes<br>
unconstrained_start = no<br>
gen_seed = -1<br>
<br>
3. see if you can reproduce the problem.<br>
<br>
4. Make the box much bigger and center your solutes (trjconv -center -pbc mol) so that you need not worry about pbc problems.<br>
<br>
5. see if you can reproduce the problem.<br>
<br>
Chris<br>
<br>
-- original message --<br>
<br>
Got it!<br>
<br>
Ok, first lines:<br>
<br>
# CONSTRAINT 3.0<br>
# Component selection: 1 1 1<br>
# nSkip 1<br>
# Ref. Group 'protein_b'<br>
# Nr. of pull groups 1<br>
# Group 1 'protein_a' Pos. 3.099513 2.982803 3.377482<br>
#####<br>
0.000000 -787.501479<br>
0.002000 -271.159600<br>
0.004000 -1147.351351<br>
0.006000 -108.722797<br>
0.008000 -97.813955<br>
0.010000 58.592018<br>
0.012000 428.034442<br>
0.014000 1022.187858<br>
0.016000 -60.867559<br>
0.018000 334.483373<br>
0.020000 1328.818408<br>
0.022000 940.307012<br>
0.024000 368.857413<br>
0.026000 1680.598490<br>
0.028000 857.879861<br>
0.030000 362.426529<br>
0.032000 1717.334105<br>
0.034000 810.192387<br>
0.036000 105.655760<br>
0.038000 1048.031839<br>
0.040000 484.148742<br>
0.042000 1312.769160<br><font color="#888888">
<br>
<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 thewww 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>
</font></blockquote></div><br>