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On 16/02/2012 1:45 AM, James Starlight wrote:
<blockquote
cite="mid:CAALQopy6CqoYjtxPOqRjcAZytobQeac5dOT6NN6HG5AbAGa=eA@mail.gmail.com"
type="cite">Mark,<br>
<br>
I've used that dimensions in accordance to some literature where
the same membrane-mimicking simulation were performed.<br>
<br>
I've tried to rise cutoffs</blockquote>
<br>
Don't, that breaks your model physics and makes it even more likely
you will encounter problems with the system dimensions becoming too
small for the cut-off!<br>
<br>
<blockquote
cite="mid:CAALQopy6CqoYjtxPOqRjcAZytobQeac5dOT6NN6HG5AbAGa=eA@mail.gmail.com"
type="cite"> and dicrease integration step but my system have been
stil crashed during npt.<br>
<br>
I'm using<br>
pcoupl = Parrinello-Rahman<br>
<br>
wich I've found in the KALP tutorial because I have not found the
same npt example file in the Biphastic tutorial :)<br>
</blockquote>
<br>
So you're following some other work and not copying their
equilibration protocol and/or model physics?<br>
<br>
<blockquote
cite="mid:CAALQopy6CqoYjtxPOqRjcAZytobQeac5dOT6NN6HG5AbAGa=eA@mail.gmail.com"
type="cite">Could you advise me another p_coup algorithm for my
Ccl4 system?<br>
</blockquote>
<br>
There's only two choices available. Manual 3.4.9 specifically warns
against one of them for equilibration. What is there to say?<br>
<br>
You should be sure to construct a simple case and get the model
physics validated. For the moment, forget about all the stuff where
you were struggling to insert more CCl4 into a box with CCl4
(probably creating a far-from-equilibrium starting configuration).
Don't try to learn to run on stilts while shaving. Learn to shave,
then to walk on stilts, then to run, then start combining them.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopy6CqoYjtxPOqRjcAZytobQeac5dOT6NN6HG5AbAGa=eA@mail.gmail.com"
type="cite">
<br>
James<br>
<br>
<div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Mark Abraham</b> <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><br>
Date: 2012/2/15<br>
Subject: Re: [gmx-users] Npt equilibration of the
membrane-mimicking CCl4 layer<br>
To: Discussion list for GROMACS users <<a
moz-do-not-send="true" href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a>><br>
<br>
<br>
<div bgcolor="#FFFFFF" text="#000000">
<div> On 15/02/2012 4:45 PM, James Starlight wrote:
<blockquote type="cite">Mark,<br>
<br>
<br>
due to hight density the volume of my system have been
slightly increased and during NPT phase I've obtained
error<br>
<br>
Fatal error:<br>
One of the box vectors has become shorter than twice the
cut-off length or box_yy-|box_zy| or box_zz has become
smaller than the cut-off.<br>
<br>
I'm using 0.9 for electrostatic and 1.4 for vdw cutofs and
the dimensions of my box was 6.5 3 3 on the initial step
and 6.6 3 3.3 before crush :)<br>
<br>
I want prevent such expansion of my system by increasing
of pressure and/ or compressibility but I have not found
exact sollution yet.<br>
</blockquote>
<br>
</div>
Your system is dangerously small for those cut-offs if your
initial density is not correct for your model physics. Your y
and z dimensions only just contain a full cut-off sphere. You
should also make sure you are following the advice about
choice of P-coupling algorithm in manual 3.4.9, and consider
using a very small integration time step. I remain unconvinced
by this thread that you have generated a starting
configuration that does not have atomic clashes.<span><font
color="#888888"><br>
<br>
Mark</font></span>
<div>
<div><br>
<br>
<blockquote type="cite"> <br>
<br>
James<br>
<br>
<br>
<div class="gmail_quote">2012/2/14 Mark Abraham <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> On 14/02/2012 11:01 PM, James Starlight
wrote:
<blockquote type="cite">This also was solved by
the some extra minimisation steps.<br>
<br>
<br>
I've forced with another problem :D<br>
<br>
During npt equilibration my system have
slightly expanded so my desired volume and
density were perturbed.<br>
<br>
I've noticed the below options in npt wich
could help me<br>
<br>
ref_p = 1 1 <br>
compressibility = 4.5e-5 <br>
<br>
i'm using this compressibility value
because I'm modelling the lipid-like
environment so I think that I must increase
pressure. Could you remind me the dependence
of pressure from density and volume for
liquids ? :)<br>
</blockquote>
<br>
</div>
Your forcefield, simulation cell contents and .mdp
settings will determine the equilibrium density.
Whether you need to do anything depends on whether
you've made a statistically significant
post-equilibration measurement of your average
density. Haphazardly increasing the reference
pressure for the coupling will reduce the volume,
but now you are simulating at that pressure. See <a
moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Pressure"
target="_blank">http://www.gromacs.org/Documentation/Terminology/Pressure</a>
for background info.<span><font color="#888888"><br>
<br>
Mark</font></span>
<div>
<div><br>
<br>
<blockquote type="cite"> <br>
James<br>
<br>
<br>
<br>
<div class="gmail_quote">2012/2/14 James
Starlight <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:jmsstarlight@gmail.com"
target="_blank">jmsstarlight@gmail.com</a>></span><br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex"> It seems
that I've fixed that problem by reduce
vdv radii for Cl during defining of my
box<br>
<br>
Eventually I've obtained box with the
desired density<br>
than I've delete vdvradii.dat for my
wor dir<br>
<br>
by when I've launched equilibration I've
oibtained<br>
<br>
Fatal error:<br>
Too many LINCS warnings (1598)<br>
If you know what you are doing you can
adjust the lincs warning threshold in
your mdp file<br>
<br>
I've never seen this before<br>
<br>
I'm using 1.o cutoff for pme and 1.4 for
vdv<br>
my LINKS parameters are<br>
<br>
; Bond parameters<br>
continuation = no ; first
dynamics run<br>
constraint_algorithm = lincs ;
holonomic constraints <br>
constraints = all-bonds ; all
bonds (even heavy atom-H bonds)
constrained<br>
lincs_iter = 1 ; accuracy of
LINCS<br>
lincs_order = 4 ; also related
to accuracy<br>
<br>
How I could solve it?<span><font
color="#888888"><br>
<br>
<br>
James</font></span>
<div>
<div><br>
<br>
<div class="gmail_quote">2012/2/14
James Starlight <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:jmsstarlight@gmail.com"
target="_blank">jmsstarlight@gmail.com</a>></span><br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">Mark,<br>
<br>
I've checked only density value<br>
<br>
with 500 molecules Ccl4 I have
density that is twisely less
that I need ( in accordance to
the literature ). Also I've
checked my box visually and
found that the box is not
properly tightly packed so I
dont know why genbox didnt add
some extra mollecules :(<br>
<br>
In other words I wounder to know
if there is any way to add some
extra molecules to the pre
defined box to make my system
more tighly packed ( to short
distance between existing
molecules and place new ones in
the new space ) ?<span><font
color="#888888"><br>
<br>
James</font></span>
<div>
<div><br>
<br>
<div class="gmail_quote">2012/2/14
Mark Abraham <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div>On 14/02/2012 4:57
PM, James Starlight
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
Justin,<br>
<br>
Firstly I've created
the box of desired
size with only 500
molecules ( I need
1000)<br>
<br>
Than I've tried to
add extra 200
molecules by means
of Genbox<br>
<br>
genbox -cp
super_box.gro -ci
Ccl4.gro -nmol 200
-o new_solv.gro<br>
<br>
but no molecules
have been added<br>
Added 0 molecules
(out of 200
requested) of Cl4<br>
</blockquote>
<br>
</div>
... then there are no
gaps large enough to
insert your molecules.
Either make gaps, or
check out genbox -h for
advice on defining the
radii.
<div><br>
<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<br>
also I've tried<br>
<br>
genbox -cp
super_box.gro -cp
Ccl4.gro -nmol 200
-o new_solv.gro<br>
</blockquote>
<br>
</div>
Two -cp options is not
what you want, and -nmol
probably only works with
-ci.
<div><br>
<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<br>
but system were
crashed with message<br>
<br>
Reading solute
configuration<br>
God Rules Over
Mankind, Animals,
Cosmos and Such<br>
Containing 2500
atoms in 500
residues<br>
Initialising van der
waals distances...<br>
<br>
WARNING: masses and
atomic (Van der
Waals) radii will be
determined<br>
based on
residue and atom
names. These numbers
can deviate<br>
from the
correct mass and
radius of the atom
type.<br>
<br>
Reading solvent
configuration<br>
"God Rules Over
Mankind, Animals,
Cosmos and Such"<br>
solvent
configuration
contains 5 atoms in
1 residues<br>
<br>
<br>
Is there any ways to
add extra mollecules
to the pre defined
box ?<br>
</blockquote>
<br>
</div>
Yes - but there has to
be room for them.<span><font
color="#888888"><br>
<br>
Mark</font></span>
<div>
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