On 10/11/2010 11:29 PM, NG HUI WEN wrote:
Hi Gmxusers,
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!
As I did not have energygrps in the initial .mdp file, I included it
this time
integrator = md
nsteps = 0
dt = 0.002
nstxout = 50000
nstvout = 50000
nstenergy = 500
nstlog = 500
Continuation = yes
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4
ns_type = grid
nstlist = 5
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
tcoupl = Nose-Hoover
tc-grps = Protein POPE SOL_CL-
tau_t = 0.1 0.1 0.1
ref_t = 323 323 323
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0
ref_p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
pbc = xyz
DispCorr = EnerPres
gen_vel = no
nstcomm = 1
comm-mode = Linear
comm-grps = Protein_POPE SOL_CL-
*energygrps = Protein SOL POPE*
I then did
1)grompp --f new.mdp --n index.ndx --c old.tpr --o rerun.tpr --p topol.top
2)trjconv --f old.trr --n index.ndx --s rerun.tpr --o rerun.trr (when
prompted, I selected "0" system)
3)mdrun --s rerun.tpr --rerun rerun.trr
I notice that the previous post
http://oldwww.gromacs.org/pipermail/gmx-users/2009-January/038968.html
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)
tpbconv -s topol.tpr -n index_P.ndx -o rerun2.tpr
Reading toplogy and shit from topol.tpr
Reading file topol.tpr, VERSION 4.0.7 (single precision)
0 steps (0 ps) remaining from first run.
You've simulated long enough. Not writing tpr file
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.
Using the g_energy command on the output energy.edr file, I got among
others, these options to choose
49 Coul-SR:Protein-Protein 50 LJ-SR:Protein-Protein
51 Coul-14:Protein-Protein 52 LJ-14:Protein-Protein
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
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.
1 Angle 2 G96Angle 3 Proper-Dih. 4
Ryckaert-Bell. 5 Improper-Dih
for 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?
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.
Also, on a slightly different note, this post
http://oldwww.gromacs.org/pipermail/gmx-users/2005-July/016307.html
suggested that the force constant of the solvent (DMSO) to be adjusted
to zero.Am I right to think that it does not apply to my case as my
protein-lipid system is solvated with SPC? (I read that SPC is rigid
water. I did not add --DFLEXIBLE in .mdp)
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.
Mark
Any help would be highly appreciated.Thanks!
HW
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