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<p class=MsoNormal><span style='color:#1F497D'>Thanks a lot Justin and Mark for
your useful input.<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Indeed Justin was right, the
quest to dissect the total energy of the system to get that contributed by the
protein alone was not trivial at all! <o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>I missed out this thread
yesterday <a
href="http://www.mail-archive.com/gmx-users@gromacs.org/msg34610.html">http://www.mail-archive.com/gmx-users@gromacs.org/msg34610.html</a>
as well as Mark’s trick to decompose bonded terms by hacking the .top
file. (However, I read from <a
href="http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy">http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy</a>
that the Coul-recip term is not decomposable regardless of the tricks used…)<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Mark, following your advice, I
added –nsteps 0 (-1 didn’t work) to tpbconv. I managed to get the interactive
prompt succesfully this time. <o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoPlainText><span style='font-family:"Courier New"'>Reading toplogy
and shit from rerun1.tpr<br>
Reading file rerun1.tpr, VERSION 4.0.7 (single precision)<br>
Setting nsteps to 0<br>
Group 0 ( System) has
100581 elements<br>
Group 1 ( Protein) has
4002 elements<br>
Group 2 ( Protein-H) has 3145
elements<br>
Group 3 ( C-alpha)
has 412 elements<br>
Group 4 ( Backbone) has 1236
elements<br>
Group 5 ( MainChain) has 1649
elements<br>
Group 6 (MainChain+Cb) has 2027 elements<br>
Group 7 ( MainChain+H) has 2039 elements<br>
Group 8 ( SideChain) has 1963
elements<br>
Group 9 ( SideChain-H) has 1496 elements<br>
Group 10 ( Prot-Masses) has 4002 elements<br>
Group 11 ( Non-Protein) has 96579 elements<br>
Group 12 ( POPE)
has 13052 elements<br>
Group 13 (
SOL) has 83523 elements<br>
Group 14 (
CL-) has 4 elements<br>
Group 15 ( Other) has
96579 elements<br>
Group 16 ( SOL_CL-) has 83527
elements<br>
Group 17 (Protein_POPE) has 17054 elements<br>
Select a group: </span><o:p></o:p></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>As suggested, I have also tried
to compare the (average) values of subset.tpr and fullsystem.tpr, these are the
total energies of:<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='color:#1F497D'><span style='mso-list:Ignore'>1)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='color:#1F497D'>System=
-1.28209 e+06<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='color:#1F497D'><span style='mso-list:Ignore'>2)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='color:#1F497D'>Protein= -9571.86<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='color:#1F497D'><span style='mso-list:Ignore'>3)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='color:#1F497D'>Lipid= -296121<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='color:#1F497D'><span style='mso-list:Ignore'>4)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='color:#1F497D'>SOL_CL= -821353<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='color:#1F497D'><span style='mso-list:Ignore'>5)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='color:#1F497D'>Other= -1.22684e+06<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>It was found that the: <o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span
style='color:#1F497D'><span style='mso-list:Ignore'>1)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='color:#1F497D'>Total energies (Protein
+ lipid + SOL_CL-) not equal to total energy of the system<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span
style='color:#1F497D'><span style='mso-list:Ignore'>2)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='color:#1F497D'>Total energies of
(Lipid + SOL_CL-) not equal to total energy of other<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span
style='color:#1F497D'><span style='mso-list:Ignore'>3)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='color:#1F497D'>Total energies of
(others + protein) not equal to total energy of the system<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>I have yet to work out the
reasons for the discrepancies, will spend some time pondering and trying to make
sense of these (and other) values.<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Thanks a bunch again!<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>HW<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:windowtext'>From:</span></b><span style='font-size:10.0pt;font-family:
"Tahoma","sans-serif";color:windowtext'> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>Mark Abraham<br>
<b>Sent:</b> Wednesday, November 10, 2010 9:08 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] mdrun -rerun: bonded interactions of protein<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>On 10/11/2010 11:29 PM, NG HUI WEN wrote: <o:p></o:p></p>
<p class=MsoNormal>Hi Gmxusers,<o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>I have been trying to run mdrun –rerun to get the
energy of the protein in my protein-lipid system. I know similar questions have
been raised on this topic before, I have tried to glean useful information from
them to solve my problem but unfortunately to no avail. Thanks for your
patience! <o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>As I did not have energygrps in the initial .mdp file, I
included it this time <o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'>integrator
= md <br>
nsteps = 0 <br>
dt =
0.002 <br>
nstxout =
50000 <br>
nstvout = 50000
<br>
nstenergy = 500 <br>
nstlog = 500 <br>
Continuation =
yes <br>
constraint_algorithm = lincs <br>
constraints = all-bonds <br>
lincs_iter = 1 <br>
lincs_order = 4 <br>
ns_type =
grid <br>
nstlist =
5 </span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'>rlist
= 1.2 <br>
rcoulomb = 1.2 <br>
rvdw =
1.2 <br>
coulombtype = PME <br>
pme_order = 4 <br>
fourierspacing =
0.16 <br>
tcoupl =
Nose-Hoover <br>
tc-grps = Protein
POPE SOL_CL- </span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'>tau_t
= 0.1 0.1 0.1 <br>
ref_t = 323
323 323 <br>
pcoupl =
Parrinello-Rahman <br>
pcoupltype =
semiisotropic </span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'>tau_p
= 5.0 <br>
ref_p = 1.0
1.0 <br>
compressibility = 4.5e-5
4.5e-5 <br>
pbc =
xyz <br>
DispCorr = EnerPres <br>
gen_vel =
no <br>
nstcomm = 1<br>
comm-mode = Linear<br>
comm-grps = Protein_POPE SOL_CL-<br>
<b>energygrps = Protein SOL POPE</b></span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'> </span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'>I
then did </span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'>1)grompp
–f new.mdp –n index.ndx –c old.tpr –o rerun.tpr
–p topol.top</span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'>2)trjconv
–f old.trr –n index.ndx –s rerun.tpr –o rerun.trr (when
prompted, I selected “0” system)</span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'>3)mdrun
–s rerun.tpr –rerun rerun.trr</span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'> </span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'>I
notice that the previous post <a
href="http://oldwww.gromacs.org/pipermail/gmx-users/2009-January/038968.html">http://oldwww.gromacs.org/pipermail/gmx-users/2009-January/038968.html</a>
suggested to use tpbconv (on rerun.tpr) and trjconv (on rerun.trr) to extract
the protein only. While it was possible to do so with trjconv, it wasn’t
feasible with tpbconv (I’m using gromacs 4.0.7) – I might have
missed out something as I did not get any prompt/output (see below)</span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'> </span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:9.0pt;font-family:"Courier New"'>tpbconv
-s topol.tpr -n index_P.ndx -o rerun2.tpr</span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'> </span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:9.0pt;font-family:"Courier New"'>Reading
toplogy and shit from topol.tpr<br>
Reading file topol.tpr, VERSION 4.0.7 (single precision)<br>
0 steps (0 ps) remaining from first run.<br>
You've simulated long enough. Not writing tpr file</span><o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><br>
Looking at the code, tpbconv checks for whether there are any more steps to
simulate before even considering letting you use it in the "create subset"
mode. You could argue that this is buggy, because the way it computes whether
there are any more steps will always indicate no more steps in such cases.
However, the workaround is to use tpbconv -nsteps -1 (as well as the other
stuff). Let me know how this goes and I'll update the documentation.<br>
<br>
<br>
<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'> </span><o:p></o:p></p>
<p class=MsoNormal>Using the g_energy command on the output energy.edr file, I
got among others, these options to choose<o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:9.0pt;font-family:"Courier New"'>49
Coul-SR:Protein-Protein
50
LJ-SR:Protein-Protein
</span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:9.0pt;font-family:"Courier New"'>51
Coul-14:Protein-Protein
52
LJ-14:Protein-Protein
</span><o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>In order to get the energy of the protein, I reckon I have
to add 49,50,51,52 (to account for the nonbonded components) and<o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><br>
I think that you can make a case either way for 1-4 interactions - they're
algorithmically similar to the other non-bonded interactions, but their
parameter values should be tightly coupled to some other of the bonded
parameters, but then in several forcefields those values are just scaled
versions of the normal ones... I'd guess most people call them non-bonded.<br>
<br>
<br>
<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-size:9.0pt;font-family:"Courier New"'>1
Angle 2
G96Angle 3
Proper-Dih. 4 Ryckaert-Bell. 5
Improper-Dih </span><o:p></o:p></p>
<p class=MsoPlainText><span style='font-size:9.0pt;font-family:"Courier New"'>f</span>or
the bonded components. However, I think 1-5 is the bonded terms for the system
and not the protein alone. Can anyone help me with this?<o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><br>
Compare values from reruns on the subset-tpr and the full-tpr. I don't know
whether/how well that works. In extremis, you should be able to reduce the .tpr
to a single interaction.<br>
<br>
<br>
<o:p></o:p></span></p>
<p class=MsoPlainText> <o:p></o:p></p>
<p class=MsoPlainText> <o:p></o:p></p>
<p class=MsoPlainText>Also, on a slightly different note, this post <span
style='font-size:10.0pt;font-family:"Courier New ;","serif"'><a
href="http://oldwww.gromacs.org/pipermail/gmx-users/2005-July/016307.html">http://oldwww.gromacs.org/pipermail/gmx-users/2005-July/016307.html</a></span>
suggested that the force constant of the solvent (DMSO) to be adjusted to zero.<span
style='font-size:10.0pt;font-family:"Courier New"'> Am I right to think that it
does not apply to my case as my protein-lipid system </span>is solvated with
SPC? (I read that SPC is rigid water. I did not add –DFLEXIBLE in .mdp)<o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><br>
That was in the context of a full-tpr rerun. The point is that atoms that have
been constrained don't contribute to relevant sums. Because you are using
constraints, there's no "Bonds" energy sum for any atom pair. Because
the DMSO was a flexible model, its bonded-interactions contributions need to be
subtracted (i.e. parameters set to zero) to get a group-wise bonded-interaction
value.<br>
<br>
Mark<br>
<br>
<br>
<o:p></o:p></span></p>
<p class=MsoPlainText> <o:p></o:p></p>
<p class=MsoPlainText>Any help would be highly appreciated.Thanks!<o:p></o:p></p>
<p class=MsoPlainText> <o:p></o:p></p>
<p class=MsoPlainText>HW<o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><<
<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>>>
<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p>
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