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>
<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">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 class="im">
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 class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div><div class="h5"><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>
<div><br>
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