On 6/20/14, 8:58 AM, Nicola Staffolani wrote:
Sorry, that's true, I am mixing things up! I am using "constraints = none"
for EnMin (and here our findings apply → Δt = .5 fs (at least)) & then
dt is irrelevant during energy minimization; only emstep matters since the
minimization algorithms are not dynamical.
"constraints = h-bonds" for the MD (and then so here I can probably safely
enough set Δt = 1 - 2 fs...
Beware that if you are using constraints in the MD, you should minimize with
constraints, otherwise the minimized structure may have bond lengths that cause
the constraint algorithm to fail.
-Justin
Thank you and sorry for being not sufficiently clear!!
Nicola
On 20 June 2014 14:36, Justin Lemkul <jalem...@vt.edu> wrote:
On 6/20/14, 8:34 AM, Nicola Staffolani wrote:
.5 fs even with h-bonds?
No, you can use 1-2 fs with h-bonds, but based on your citation of a
previous post that did not use constraints and then you said:
"And I was thinking that we should remove the constraints if we want to
see the appropriate oscillations!"
it sounded like you would not be using constraints.
-Justin
On 20 June 2014 14:29, Justin Lemkul <jalem...@vt.edu> wrote:
On 6/20/14, 4:01 AM, Nicola Staffolani wrote:
On 19 June 2014 23:59, Justin Lemkul <jalem...@vt.edu> wrote:
On 6/19/14, 10:05 AM, Nicola Staffolani wrote:
Dear Justin,
thank u 4 replying!
On 19 June 2014 15:04, Justin Lemkul <jalem...@vt.edu> wrote:
On 6/19/14, 4:11 AM, Nicola Staffolani wrote:
Dear GMX community,
I am running simulations of a solvated protein on a (frozen) Au
substrate,
but I think that my question is so basic that it falls outside the
details
of my case...
So, the question is: when I prepare the system by minimizing the
energy,
should I set constraints = all_bonds, h_bonds or none?
What was your force field parametrized to use? Most commonly,
modern
force fields constrain bonds involving H, though all bonds are
frequently
constrained in practice because the differences are generally small
and
the
rigid representation of a bond is considered by many to be a more
realistic
representation of the ground state than a harmonic function.
I do not understand your question... Do you mean which force field I
am
using? In this case the answer is gromos43a1...
Constraining all bonds is common with Gromos96 parameter sets. I
know
that 53a6 was parametrized with all bonds constrained; I am not sure if
the
full details of 43a1 were ever published. If someone else knows,
please
chime in. The oldest public reference I know of for Gromos96 is a
paper
about the software suite in general, but not the original
parametrization
protocol.
IMHP, I should set it to all_bonds, otherwise I may risk that the
system's
energy minimum corresponds to a configuration very different from
the
initial one... However, I saw somebody is using constraints = none
and
I
was wandering why...
Without context, answering that is impossible.
I see... How can I better describe the context ? Which info do u
need?
I have seen setting the constraints to none with the same very
system as
mines (solvated azurin on Au
layers) where the ff used was again gromos43a1...
The context to which I refer is: what were the goals of the study?
If
one
wants to examine, for instance, vibrational spectra, it would be
inappropriate to apply constraints (and you'd be forced to use a very
small
time step). For normal MD investigations, constraints are used to
increase
the time step for better throughput. My comment about context is also
a
general one. People often mention previous posts without providing
links
or looking at the whole thread. There may be very specific reasons
for a
particular approach, or it may turn out that the posted settings were
wrong
;)
Thanks for explaining! Indeed we are in a early phase of our study
and
are
interested in the vibrational (Raman) spectra (!!) of Cu-ligands; we
want
to see whether we are able to reproduce the experimental spectra in
order
to validate our model and then go further... And I was thinking that we
should remove the constraints if we want to see the appropriate
oscillations!
It is also very interesting your comment about the relation between time
step duration and aim of the MD simulation: I had been suggested to use
Δt
= 0.002 ps, but then I had issues with the frozen Au layers and changed
it
to 0.001 ps. Afterwards, in my last runs, I changed some other
parameters
and decided to give a try again to 0.002 ps, but it seems more
appropriate
- thanks to your comment - to switch back to 0.001 ps...
Without constraints, you may need an even smaller time step, 0.5 fs at
most, for proper energy conservation.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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