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On 10/11/2010 11:29 PM, NG HUI WEN wrote:
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<div class="WordSection1">
<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: 10pt;
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 <o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
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- <o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
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 <o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
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<o:p></o:p></b></span></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">I
then did <o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">1)grompp
–f new.mdp –n index.ndx –c old.tpr –o rerun.tpr –p
topol.top<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">2)trjconv
–f old.trr –n index.ndx –s rerun.tpr –o rerun.trr (when
prompted, I selected “0” system)<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">3)mdrun
–s rerun.tpr –rerun rerun.trr<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">I
notice that the previous post <a moz-do-not-send="true"
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)<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 9pt;
font-family: "Courier New";">tpbconv
-s topol.tpr -n index_P.ndx -o rerun2.tpr</span><span
style="font-size: 10pt; font-family: "Courier
New";"><o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 9pt;
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></p>
</div>
</blockquote>
<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>
<blockquote
cite="mid:EE6BA5FF4C277348A3A297EDC1D54DC5C330B3@wsexbe2.nottingham.edu.my"
type="cite">
<div class="WordSection1">
<p class="MsoPlainText"><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";"><o:p> </o:p></span></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: 9pt;
font-family: "Courier New";">49
Coul-SR:Protein-Protein
50
LJ-SR:Protein-Protein
<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 9pt;
font-family: "Courier New";">51
Coul-14:Protein-Protein
52
LJ-14:Protein-Protein
<o:p></o:p></span></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</p>
</div>
</blockquote>
<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>
<blockquote
cite="mid:EE6BA5FF4C277348A3A297EDC1D54DC5C330B3@wsexbe2.nottingham.edu.my"
type="cite">
<div class="WordSection1">
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 9pt;
font-family: "Courier New";">1
Angle 2
G96Angle 3
Proper-Dih. 4 Ryckaert-Bell. 5
Improper-Dih <o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 9pt;
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?</p>
</div>
</blockquote>
<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>
<blockquote
cite="mid:EE6BA5FF4C277348A3A297EDC1D54DC5C330B3@wsexbe2.nottingham.edu.my"
type="cite">
<div class="WordSection1">
<p class="MsoPlainText"><o:p></o:p></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: 10pt; font-family: "Courier
New";"><a class="moz-txt-link-freetext" 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: 10pt; 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>
</div>
</blockquote>
<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>
<blockquote
cite="mid:EE6BA5FF4C277348A3A297EDC1D54DC5C330B3@wsexbe2.nottingham.edu.my"
type="cite">
<div class="WordSection1">
<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>
</div>
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