Ok, now here we go:
Energy Average RMSD Fluct. Drift
Tot-Drift
---
Bond2.06511 0.0619081 0 0.0891128
22.2784
Angle 2.62252 0.06
Hi David.
Thanks a lot. Just trying it now.
The mistake of the g_energy was something I sould have expected: I use an
old Suse version, which *has* gromacs 3.2 installed by standard. The paths
where getting that one instyead of my actual one. I completelly forget that,
specially cause for no rea
Jones de Andrade wrote:
Hi David.
Well, as long as I can remember, I pushed the last gromacs sources at
time (3.3.1) and just installed it. Anyway, mdrun tells me it is 3.3 and
g_energy says it is 3.2.1 (in the run headers). I expected this to be
normal, or could I have run in some kind of un
Hi David.
Well, as long as I can remember, I pushed the last gromacs sources at time (
3.3.1) and just installed it. Anyway, mdrun tells me it is 3.3 and g_energy
says it is 3.2.1 (in the run headers). I expected this to be normal, or
could I have run in some kind of unnexpected or unremembered p
Jones de Andrade wrote:
Hi all.
First, I would like to apologize for the previous message. Maybe I've
been too "harsh"? Sorry for that.
Second, I would like to list all the energetic contributions for one
(same system, different run) run that g_energy allowed me to get:
Energy
Jones de Andrade wrote:
Hi all.
First, I would like to apologize for the previous message. Maybe I've
been too "harsh"? Sorry for that.
Second, I would like to list all the energetic contributions for one
(same system, different run) run that g_energy allowed me to get:
Energy
Hi all.
First, I would like to apologize for the previous message. Maybe I've been
too "harsh"? Sorry for that.
Second, I would like to list all the energetic contributions for one (same
system, different run) run that g_energy allowed me to get:
Energy Average RMSD
Hi David.
Just tried it, and it isn't getting not even funny!
Ok, without using the nmol flag, calculated total, potential and kinetic
energy.
Results:
Potential -5109.4669.1951 68.569 0.128686
32.1718
Kinetic En. 3838.2167.941767.9418 -9.0475
Jones de Andrade wrote:
Hi David!
Ha, so there is something extra? Thanks a lot :) I knew I was
forgeting something.
So how should I deal with it? I mean, what are the contibutions that are
inside the "Potential" option of g_energy? Does it include all
corrections, disp.corr. ones als
Hi David!
Ha, so there is something extra? Thanks a lot :) I knew I was
forgeting something.
So how should I deal with it? I mean, what are the contibutions that are
inside the "Potential" option of g_energy? Does it include all corrections,
disp.corr. ones also, or there is something miss
Jones de Andrade wrote:
Hi Mark.
Haven't got exactly what you said. So let me rephrase myself:
The CF4 molecule doesn't have dihedrals nor intramolecular LJ and
coulombic contributions.
What kind of contribution am I missing that makes potential energy minus
bond stretching minus angle bend
Hi Mark.
Haven't got exactly what you said. So let me rephrase myself:
The CF4 molecule doesn't have dihedrals nor intramolecular LJ and coulombic
contributions.
What kind of contribution am I missing that makes potential energy minus
bond stretching minus angle bending *different* from Lj + co
> The intermolecular energy in the liquid should no be equal to the sum of
> the
> LJ, coulomb(SR, coulb(LR) and Disp Correction? And, that correct,
> shouldn't
> it be equal also to the potential energy minus bond minus angle bending
> energies? What am I missing, that is making me have both diff
Hi all.
Well, I have a question on the usage of g_energy.
I'm simulationg a really small test molecule, CF4. No problems with
parameter, even nmol flag was used.
My question(s) is a bit of usage or interpretation.
The intermolecular energy in the liquid should no be equal to the sum of the
LJ,
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