By the way I also wounder to know how I could keep my system after
equilibration.
E.g I've equilibrated CCl4+water system and obtain stabile system on
desired timescale.
Than I've used genbox to merge my pre-oriented peptide with the
pre-equilibrated system.
genbox -cp peptide_newbox.gro -cs CC
On 17/02/2012 5:33 PM, James Starlight wrote:
Mark,
The pure Ccl4 cube was expanded in X dimension during npt phase.
So assuming you simulated long enough to have reasonable convergence,
your model is not stable at the initial volume with whatever that
reference pressure was.
By the way
Mark,
The pure Ccl4 cube was expanded in X dimension during npt phase. By the way
I've been able to prevent it by increasing the ref_p of X up to 5 ussing
semiisotropic pcoupltype
By when I've inserted peptide on the npt of that system my Ccl4 box was
expanded on Z rapidly.
Might this way to
On 17/02/2012 4:46 PM, James Starlight wrote:
So my problem still is
1) During npt without peptide my Ccl4 system expan rapidly in
X-dimension. That produce error on 2nd ns of equilibration
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz h
he 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,
>&g
shaving. Learn to shave, then to walk on stilts, then to run,
> then start combining them.
>
> Mark
>
>
>
> James
>
> -- Forwarded message --
> From: Mark Abraham
> Date: 2012/2/15
> Subject: Re: [gmx-users] Npt equilibration of the membrane-
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* <mailto:mark.abra...@anu.edu.au>>
Date: 2012/2/15
wich I've found in the KALP tutorial because I have not found the same npt
example file in the Biphastic tutorial :)
Could you advise me another p_coup algorithm for my Ccl4 system?
James
-- Forwarded message --
From: Mark Abraham
Date: 2012/2/15
Subject: Re: [gmx-users] Npt
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
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 elect
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
I assume that you energy minimisd the system, but still have atomic clashes?
One thing which helped me in a similar case, was a short simulation at
low temperature with a really small timestep (about 3-5 magnitudes
smaller than the normal timestep). With this the atoms which clashes
move away
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
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 kno
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 :(
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
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
Hi,
i second Justins seond idea (creating a small box of equilibrated CCl4
and then fill the simulation box via the -cs option).
Depending if you have other molecules in your system, make the
simulation box a little bit bigger, because you will get some holes. In
the subsequent NPT simulation t
James Starlight wrote:
Justin,
2012/2/6 Justin A. Lemkul mailto:jalem...@vt.edu>>
Some simple calculations using the desired density and the box
dimensions (to get the volume) will tell you exactly how many
molecules you need. If you only "suppose" you've got a reasonable
n
Justin,
2012/2/6 Justin A. Lemkul
>
> Some simple calculations using the desired density and the box dimensions
> (to get the volume) will tell you exactly how many molecules you need. If
> you only "suppose" you've got a reasonable number, there are better ways to
> be sure ;)
>
>
In accordan
James Starlight wrote:
Justin,
I've built my system in accordance to the first way from your Biphgastic
system tutorial.
I've defined system with slight biger ( on 1 nm in each dimension)
dimensions that I needed and place maximym CCl4 molecules in that box by
genbox -ci ccl4.gro -nmol
Justin,
I've built my system in accordance to the first way from your Biphgastic
system tutorial.
I've defined system with slight biger ( on 1 nm in each dimension)
dimensions that I needed and place maximym CCl4 molecules in that box by
genbox -ci ccl4.gro -nmol 900 -box 9.6 7.5 4 -o new_box.
James Starlight wrote:
Justin,
Larger cutoffs would not only make the problem worse (read the error
message carefully and consider the minimum image convention), but it
would also potentially break the validity of the force field model.
The vdW cutoff for Gromos96 should be 1
Justin,
Larger cutoffs would not only make the problem worse (read the error
> message carefully and consider the minimum image convention), but it would
> also potentially break the validity of the force field model. The vdW
> cutoff for Gromos96 should be 1.4 nm, not 0.9 nm, in any case.
Thi
James Starlight wrote:
Dear Gromacs Users!
I have problems during npt equilibration of my solvent box with the CCl4
solvent (I'm preparing this hydrophobic layer for further
membrane-mimicking system).
As the result I want to obtain density value ~ 1.5 for such box but
between 2 and 3 n
Dear Gromacs Users!
I have problems during npt equilibration of my solvent box with the CCl4
solvent (I'm preparing this hydrophobic layer for further
membrane-mimicking system).
As the result I want to obtain density value ~ 1.5 for such box but between
2 and 3 ns ( where the desity was 1.3) o
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