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!
Exactly how would define "the energy of the protein?" This is a question that
gets posted very frequently, and the answer is always the same - it doesn't
correspond to any useful quantity, not that you can extract one, anyway.
As you've noticed, energygrps can only be used to decompose short-range
nonbonded interactions, not bonded or long-range interactions. You will have
energy terms associated with the Coul.-recip. term from PME; how do you deal
with that? As you can see, it is not a trivial exercise.
-Justin
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
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
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?
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)
Any help would be highly appreciated.Thanks!
HW
<<
This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it.
Please do not use, copy or disclose the information contained in this
message or in any attachment. Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.
This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system: you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
permitted by UK & Malaysia legislation.
>>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
