On 16/02/2012 1:45 AM, James Starlight wrote:
Mark,
I've used that dimensions in accordance to some literature where the
same membrane-mimicking simulation were performed.
I've tried to rise cutoffs
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!
and dicrease integration step but my system have been stil crashed
during npt.
I'm using
pcoupl = Parrinello-Rahman
wich I've found in the KALP tutorial because I have not found the same
npt example file in the Biphastic tutorial :)
So you're following some other work and not copying their equilibration
protocol and/or model physics?
Could you advise me another p_coup algorithm for my Ccl4 system?
There's only two choices available. Manual 3.4.9 specifically warns
against one of them for equilibration. What is there to say?
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.
Mark
James
---------- Forwarded message ----------
From: *Mark Abraham* <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
Date: 2012/2/15
Subject: Re: [gmx-users] Npt equilibration of the membrane-mimicking
CCl4 layer
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
On 15/02/2012 4:45 PM, James Starlight wrote:
Mark,
due to hight density the volume of my system have been slightly
increased and during NPT phase I've obtained error
Fatal error:
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.
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 :)
I want prevent such expansion of my system by increasing of pressure
and/ or compressibility but I have not found exact sollution yet.
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.
Mark
James
2012/2/14 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
On 14/02/2012 11:01 PM, James Starlight wrote:
This also was solved by the some extra minimisation steps.
I've forced with another problem :D
During npt equilibration my system have slightly expanded so my
desired volume and density were perturbed.
I've noticed the below options in npt wich could help me
ref_p = 1 1
compressibility = 4.5e-5
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 ? :)
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
http://www.gromacs.org/Documentation/Terminology/Pressure for
background info.
Mark
James
2012/2/14 James Starlight <jmsstarli...@gmail.com
<mailto:jmsstarli...@gmail.com>>
It seems that I've fixed that problem by reduce vdv radii
for Cl during defining of my box
Eventually I've obtained box with the desired density
than I've delete vdvradii.dat for my wor dir
by when I've launched equilibration I've oibtained
Fatal error:
Too many LINCS warnings (1598)
If you know what you are doing you can adjust the lincs
warning threshold in your mdp file
I've never seen this before
I'm using 1.o cutoff for pme and 1.4 for vdv
my LINKS parameters are
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
How I could solve it?
James
2012/2/14 James Starlight <jmsstarli...@gmail.com
<mailto:jmsstarli...@gmail.com>>
Mark,
I've checked only density value
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 :(
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 ) ?
James
2012/2/14 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
On 14/02/2012 4:57 PM, James Starlight wrote:
Justin,
Firstly I've created the box of desired size
with only 500 molecules ( I need 1000)
Than I've tried to add extra 200 molecules by
means of Genbox
genbox -cp super_box.gro -ci Ccl4.gro -nmol 200
-o new_solv.gro
but no molecules have been added
Added 0 molecules (out of 200 requested) of Cl4
... 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.
also I've tried
genbox -cp super_box.gro -cp Ccl4.gro -nmol 200
-o new_solv.gro
Two -cp options is not what you want, and -nmol
probably only works with -ci.
but system were crashed with message
Reading solute configuration
God Rules Over Mankind, Animals, Cosmos and Such
Containing 2500 atoms in 500 residues
Initialising van der waals distances...
WARNING: masses and atomic (Van der Waals) radii
will be determined
based on residue and atom names. These
numbers can deviate
from the correct mass and radius of the
atom type.
Reading solvent configuration
"God Rules Over Mankind, Animals, Cosmos and Such"
solvent configuration contains 5 atoms in 1 residues
Is there any ways to add extra mollecules to the
pre defined box ?
Yes - but there has to be room for them.
Mark
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