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On 14/07/2010 6:40 AM, Moeed wrote:
<blockquote
cite="mid:AANLkTilC6ccOyGoOwmwQg__T1a19PENF5agEQlcJScsM@mail.gmail.com"
type="cite">Hello, <br>
<br>
I followed the hints. I did several NPT runs and I found out pressure
above 100 eg 120 bar gives final boxsize close to volume of box I want.
But I dont know why pressure given by g_energy is totally different. <br>
<br>
1- I looked at values in xvg file and I notoced pressre starts froma
very low value, also takes negative and postive values. If I am doing
NPT why P is changing ?<br>
</blockquote>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Terminology/Pressure">http://www.gromacs.org/Documentation/Terminology/Pressure</a><br>
<blockquote
cite="mid:AANLkTilC6ccOyGoOwmwQg__T1a19PENF5agEQlcJScsM@mail.gmail.com"
type="cite">2- at the end of xvg file I see final dimensions are 2*2*2
. Also I checked the size in ngmx and I see that long chain is
compressing very nicely and takes a very convoluted conformation in a
very small size. I selected 1000 ps but after 727 ps simulation stops
(it seems box size can not be reduced further).However, When I open the
gro file PE60_after_MD dimensions are 22*22*22! :( why is this
happening?<br>
</blockquote>
We can't really tell, because we can't see what data you're basing this
assessment on. My first guess is that you were looking at a PDB file,
and 22A is around 2nm.<br>
<br>
"Simulation stops"? What does that mean?<br>
<blockquote
cite="mid:AANLkTilC6ccOyGoOwmwQg__T1a19PENF5agEQlcJScsM@mail.gmail.com"
type="cite"><br>
<br>
Energy Average RMSD Fluct. Drift
Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Angle 725.016 41.3878 36.4581 0.0790551
67.8611<br>
Ryckaert-Bell. 231.804 29.096 25.866
0.0537685 46.155<br>
LJ-14 161.418 8.09535 7.98175 0.00545371
4.68147<br>
Coulomb-14 -87.8111 8.74814 7.24162 0.0198065
17.0019<br>
LJ (SR) -145.619 82.9315 38.527 -0.296365
-254.401<br>
Coulomb (SR) 190.015 14.0939 11.1829 -0.0346165
-29.7149<br>
Potential 1074.82 73.9367 60.258 -0.172898
-148.416<br>
Kinetic En. 899.733 29.9816 29.9813 0.000554359
0.475863<br>
Total Energy 1974.56 67.628 52.4374 -0.172344
-147.94<br>
Temperature 299.757 9.98875 9.98864
0.000184692 0.15854<br>
<b>Pressure (bar) -1.43379 141.354 141.205
-0.0261305 -22.4305</b><br>
</blockquote>
<br>
All this means is that over the course of the simulation the observed
pressure was negative - which is what you expect for a system that got
dramatically smaller, and then wasn't allowed to equilibrate under more
normal pressure-coupling.<br>
<br>
<blockquote
cite="mid:AANLkTilC6ccOyGoOwmwQg__T1a19PENF5agEQlcJScsM@mail.gmail.com"
type="cite">Cons. rmsd () 5.12607e-06 4.18181e-07
3.98738e-07 5.08597e-10 4.3658e-07<br>
Box-X 10.7454 7.6259 2.33711 -0.0292936
-25.1457<br>
Box-Y 10.7454 7.6259 2.33711 -0.0292936
-25.1457<br>
Box-Z 10.7454 7.6259 2.33711 -0.0292936
-25.1457<br>
Density (SI) 32.6368 57.0897 38.1186 0.171508
147.222<br>
pV -5.00443 428.488 428.332 -0.0466916
-40.0802<br>
Vir-XX 321.928 424.592 424.396 0.051996
44.6335<br>
Mu-X 0.00138297 0.33292 0.332911 -9.74152e-06
-0.00836214<br>
Lamb-System 1.00002 0.000363012 0.000363011
-3.17825e-09 -2.72822e-06<br>
Heat Capacity Cv: 12.4926 J/mol K (factor = 0.00111041)<br>
<br>
3- The systems seems not to be equilibrated yet. eg LJ SR remains
constant for a while and goes down and its not reaching a plateau after
720 ps (where simulation stops). <br>
</blockquote>
<br>
Yes, it's almost certainly not equilibrated. You've coerced a serious
change to the conformation in an eyeblink. Give it some time under
normal conditions :-)<br>
<br>
<blockquote
cite="mid:AANLkTilC6ccOyGoOwmwQg__T1a19PENF5agEQlcJScsM@mail.gmail.com"
type="cite">4- When I choose p 200bar , compression continues till 420
ps. Actually chain takes a specific conformation in such a way that it
can not get compressed further and simulation stops even before former
trial (p 120 bar).<br>
a simple question:<br>
5- About tc groups in mdpfile: actually I see people having names like
protein SOL as their groups but I am wondering how I can set the name
"polymer". I thought this comes form the [system] or [molecule] in top
file but its not so (or thought may names are coming form index file).
If I want to add hexane to PE and calculate energies I need to have
these two groups separately. for PE I have three residues Eth EthB
EthE.Could you please tell me how can I include them in one single
group 'Polymer"? and use this name in mdp file?<br>
</blockquote>
You do not want (or need) to use the same groups for T-coupling and
energy monitoring. Under normal circumstances, GROMACS default
definitions for protein and SOL just work. Under your circumstances,
they probably won't. So, use make_ndx to make your polymer group, and,
if appropriate, a hexane group. Then T-couple to SOL, polymer and
hexane. If they're small, it might be more appropriate to merge hexane
and/or polymer into one of the other groups.<br>
<br>
If you're really sure you want to monitor energies on subsets of the
hexane group, then go and make those subsets.<br>
<br>
Mark<br>
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