rasoul nasiri wrote:
Dear All,
Hello
I understand one can adjust distance of between solvent molecules by
genbox command and -vdwd but I don't know, how do it between the
solutes?
If you want to place several identical solutes with genbox -ci, then you
could copy the file vdwradii.dat
Dear All,
Hello
I understand one can adjust distance of between solvent molecules by genbox
command and -vdwd but I don't know, how do it between the solutes?
Thanks for helping!
Rasoul
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rasoul nasiri wrote:
Dear All,
Hello
I understand one can adjust distance of between solvent molecules by
genbox command and -vdwd but I don't know, how do it between the solutes?
Position your solutes using editconf -center, then add solvent.
-Justin
Thanks for helping!
Rasoul
Dear Justin,
Hello again
Thanks for the message. I want to increase the distance between solutes in
simulation box before MD simulation. How can I do it?
Rasoul
On Sat, Apr 17, 2010 at 5:16 PM, Justin A. Lemkul jalem...@vt.edu wrote:
rasoul nasiri wrote:
Dear All,
Hello
I understand
rasoul nasiri wrote:
Dear Justin,
Hello again
Thanks for the message. I want to increase the distance between solutes
in simulation box before MD simulation. How can I do it?
You can't. If you know you need a certain distance, that should be part of your
planning :) I suppose you
Justin A. Lemkul wrote:
rasoul nasiri wrote:
Dear Justin,
Hello again
Thanks for the message. I want to increase the distance between
solutes in simulation box before MD simulation. How can I do it?
You can't. If you know you need a certain distance, that should be part
of your
Hi,
Thanks for the replies.
Since I want to increase distance among co-solvents with themselves and with
solutes, i must firstly fill the co-solvents along solutes and solvents
after that i remove solvent, finally by edittconf -translate the co-solvents
uniformally is distributed in the
rasoul nasiri wrote:
Hi,
Thanks for the replies.
Since I want to increase distance among co-solvents with themselves and
with solutes, i must firstly fill the co-solvents along solutes and
solvents after that i remove solvent, finally by edittconf -translate
the co-solvents uniformally is
Thanks for the information.
Because of haven't satisfactory model from my co-solvent and I have to add
it randomly along with the solvent by genbox -ci -nmol.
the reason of this criteria relate to crash of system
(solute+co-solvent+solvent) in the first step of simulation, because small
distance
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