On Wed, 12 Dec 2007, Claus Valka wrote:
Dear Sir,
I would try to be more precise.
example1 mdp file:
rlist = (greater or equal to rvdw)
vdw-type = Switch
rvdw-switch=5.56
rvdw=8.9
are you aware that gromacs usues nm for distance?
you can find the functional form of the shift/switch function in the
manual.
Between the value 5.56 and 8.9 gromacs uses cubic
spline?
example2 mdp file:
rlist=5.56
vdw-type = Cut-off
rvdw-switch=0 (this value here should be irrelevant)
rvdw=8.9
Gromacs uses cubic spline after the value 8.9 till LJ
to go to zero?
And which is the difference of rlist if someone uses
vdw-type = Cut-off instead of vdw-type = Switch? It
would have been nice to have images of these options
so as to be better understood.
Because it is stated in the manual:
rlist: (1) [nm]
cut-off distance for the short-range neighbor list
and also:
Switch
...The neighbor search cut-off rlist should be 0.1 to
0.3 nm LARGER than rvdw...
Isn't this a little bit contradictive?
As far as twin cutoffs are concerned if we want to
find out the total energy of the non bonded
interactions we have to add LJ-14 + LJ(SR) + LJ(LR)?
With tabulated potentials can I use different cutoffs
for different types of atoms? Judging from your answer
about system wide cutoffs I understand that even
though I might use tabulated potentials, I won't be
able to use different cutoffs for the different types
of atoms I have. Am I correct?
Yours Sincerely,
Nikos
--- Mark Abraham <[EMAIL PROTECTED]> schrieb:
Claus Valka wrote:
Hello,
3rd question: Which is the difference between the
S(hort)R(ange) LJ and LJ 1-4? For me the short
range
interactions are the 1-4LJ, yet it seems that this
is
not the case.
GROMACS uses twin-range cutoffs (see manual), so
LJ-SR is inside the
shorter cutoff, and LJ-LR is outside.
4th question: I want after 1,45*σ till
2,33*σ to use the cubic spline in such a way
that
the LJ potential will go smoothly to zero at
2,33σ. If I use the biggest σ I have,
then
in the mdp file rvdw-switch=5.56 and rvdw=8.9.
Between
these two values does the cubic spline work as a
switch function using vdw-type = Switch ?
Please find a way to describe your problem with
plain ASCII text.
5th question: Given the above if I use vdw-type
=Cut-off and rvdw=8.9 then gromacs will use cubic
spline till the LJ will reach zero for a value
greater
than 8.9, yet to me uknown? If this is not the
case
how LJ goes to zero with this option?
I don't understand what you're asking.
6th question: If I want to use a quintic spline
between 1,45*σ till 2,33*σ(cut-off
value)
for the different combination of atoms(they have
different ε and σ), then should I use a
tabulated potential? And if I do that which will
be
the meaning of cutoffs in the mdp file as I would
like
them to be different for each of the different
types
of atoms I have? Can I use different cut-offs for
the
different types of atoms I have?
The cut-offs are a system-wide property.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the
list. Use the
www interface or send it to
[EMAIL PROTECTED]
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
Jetzt Mails schnell in einem Vorschaufenster überfliegen. Dies und viel
mehr bietet das neue Yahoo! Mail - www.yahoo.de/mail
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
