Nick wrote:
One last question!
1- So what are the 12 energy terms I get by passing index file onto step
2 below? I ignored rerun! what does rerun does?
I don't know what 12 terms you're referring to. You'll get A-A, A-B, and B-B
short-range nonbonded terms, the exact enumeration of which will depend on the
settings in your .mdp file.
The -rerun function is explained in the manual, or alternatively "mdrun -h." I
assumed (perhaps incorrectly) that you had generated a trajectory using some
energygrps and you wished to make changes after the fact in the way the
nonbonded potential was decomposed.
2- So I dont have to include index file in mdrun initially..In brief
what I need is:
step 1 grompp .....(no index)
step 2 mdrun -s old.tpr -o old.trr -c *.gro
(grompp and mdrun as usual) then:
grompp -f energygroups.mdp -c .top -o
new.tpr * -n index.ndx*
mdrun *-s new.tpr -rerun old.trr...*
Please confirm. Many thanks for your help.
You don't necessarily need the -rerun function if you plan ahead. Using mdrun
-rerun is only useful in the case that you haven't set your energygrps properly
and you don't want to completely run the simulation over again.
-Justin
On 22 February 2011 17:35, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Nick wrote:
Dear Justin,
Thanks for your reply and Sorry for asking naive questions...
1- I am looking at all possible interaction energies between
components A and B. that is A-A AB and BB. So interaction
between single chains is not what I want. With this I think my
initial approach was right. That is putting all atoms of 3 A
chains under [A] and the same all solvent atoms under [B] and
setting A and B as energy groups in mdp. Am I right?
If you don't want your energies on a per-chain basis, then yes.
2- One more thing bout question 3: I am passing on index.ndx to
mdrun command.
with the index file I talked about I am getting the follwoing
for AA AB and BB: LJ SR, LJ 1-4 coulomb SR and 1-4. (i.e 12
energy terms).
I think you say I need rerun since you assumed I did not pass it
onto mdrun. right?
You need to create a new .tpr file that has the desired groups
specified in it. You pass the new .tpr file to mdrun, in
conjunction with your old trajectory (i.e., mdrun -s new.tpr -rerun
old.trr).
3- to get intermolecular interaction energies say for AA I need
to add up LJ SR+coulomb SR? say +123-50=73 ? or just take
absolute values : 123+50=173 ?
Sign matters a lot. Positive is repulsive, negative is attractive.
You can't just switch them arbitrarily.
-Justin
Thanks,
Nick wrote:
Dear experts,
1- I am trying to get interaction energies between solute (3
chains A) and solvent 50 molecules B. In the index file I
created two groups: one for all atoms of [A] and and [B]
for all
solvent molecules. and by setting A and B as energy groups in
mdp file I am getting break down as A-A, A-B and B-B with
g_energy.
I am a little confused as I dont know if I need to create
different groups for my solute to get interaction
energies A-A,
A-B and B-B. I mean do I need to have [A1] for solute chain 1
...[A3] for chain 3?
If you want a breakdown of per-chain energetics, then yes,
specify
each chain as a group. The programs will only do what you tell
them, nothing more, nothing less.
and then sent A1, A2, A3 in mdp file and run g_energy? if
I need
to specify different chains, then to get say A-A should I
average over all possible A1-A2, A1A3, A2-A3, A1-B,
A2,B...? I
am really confused ..
Theoretically, the short-range terms should sum, not average.
2- I know it is naive question but What does A1-A1 mean?
How can
one chain interact with itself?
Without knowing what the chain is, no one can answer this.
Generally, any atoms that are within the short-range cutoff and
further away than nrexcl bonds contribute to short-range
interactions. Long-range interactions (i.e., PME terms)
happen too,
but you can't decompose that term with energygrps.
3- Do I need to use mdrun - rerun option to get beakdown
or just
g_energy gives what I need?
You need to -rerun. g_energy does not take an index file, and it
only analyzes existing groups, it cannot derive new ones.
-Justin
Thanks for your help
Paniz
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
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
========================================
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