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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