On 9/17/18 8:37 AM, Vytautas Rakeviius wrote:
And what about OPLS-AA/L if I do nvt equilibration of my protein in water
with it is it OK to do constraints = all-bondsall the time like I
am used to do?
I would encourage you to examine the primary literature for the force
field, understand what its conventions are, and apply whatever is
correct for that force field.
-Justin
On Monday, September 17, 2018, 3:18:51 PM GMT+3, Justin Lemkul
<jalem...@vt.edu> wrote:
On 9/17/18 8:12 AM, Vytautas Rakeviius wrote:
Can you explain more to us when it is not appropriate to constrain all bonds
during nvt equilibration?
The use of constraints is not tied to the statistical mechanical
ensemble or the simulation process (equilibration, production, etc).
Constraints are a convention of force fields. For example, it is stated
in the primary literature for the GROMOS force fields that all bonds are
constrained. That is an assumption within the physical model, and proper
use of that force field dictates that the user should follow that
convention. For CHARMM, only bonds to H are to be constrained, because
the bond vibrations are expected to be present. Every intramolecular
interaction is linked - if you violate the force field convention with
respect to bonds, then the angle vibrations are inconsistent with the
parametrization, the dihedrals (which are tied to both bonds and angles)
are not necessarily employed correctly, etc.
The main point: every element of a force field, from its cutoffs, water
model, use of constraints, etc. is linked. While there are deviations
from this "absolute" statement in certain cases, consider this a pretty
strong rule for doing accurate and reliable simulations. There are not
as many choices to be made as one might expect.
-Justin
On Monday, September 17, 2018, 3:06:56 PM GMT+3, Justin Lemkul
<jalem...@vt.edu> wrote:
On 9/17/18 8:04 AM, Vytautas Rakeviius wrote:
I think your attachment to email was lost during re-transfer and it would
be nice to see that, but I think what you need is:constraints =
all-bondsIn that mdp file.
That depends on the force field convention. It is not universally
appropriate to constrain all bonds (and certainly should not be the
"solution" to just "make the warning go away"), and the warning from
grompp may not actually be the source of any problem.
-Justin
On Friday, September 14, 2018, 4:07:43 PM GMT+3, Gonzalez Fernandez,
Cristina <cristina.gonzalezf...@unican.es> wrote:
Dear Gromacs users,
I am trying to perform a nvt equilibration, but when I generate the .tpr file I
get a warning indicating that a bond is oscillating too fast:
The bond in molecule-type MOL_1 between atoms 38 C21 and 39 O22 has an
estimated oscillational period of 2.4e-02 ps, which is less than 5 times the
time step of 1.5e-02. Maybe you forgot to change the constraints mdp option.
I have ignored it with the -maxwarn option and I obtain the .tpr file. However,
when I run the simulation I obtain this error?
Too many LINCS warnings (1630)
Are the error and the warning related? How could I solve the Lincs error and
the warning?
I attach the .mdp file.
Thank you in advance,
C.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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