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 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>Could you advise me another p_coup algorithm for my Ccl4 system?<br>
<br>James<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Mark Abraham</b> <span dir="ltr"><<a 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 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 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 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 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 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 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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