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<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 <o:p></o:p></span></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- <o:p></o:p></span></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 <o:p></o:p></span></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<o:p></o:p></b></span></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'>I
then did <o:p></o:p></span></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<o:p></o:p></span></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)<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-size:10.0pt;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:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></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)<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></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><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></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=MsoPlainText><span style='font-size:10.0pt;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:9.0pt;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:9.0pt;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<o:p></o:p></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 <o:p></o:p></span></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=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"'>http://oldwww.gromacs.org/pipermail/gmx-users/2005-July/016307.html</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=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>
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