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one problem about box setting
#5738 03/09/05 03:38 AM
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Dear all,
I want to set a box without PBC, just only a box. My purpose is I just want my molecule to move in the box. Here is my setting,
...........
set 7 130.000
set 8 300.000
set 9 130.000

crystal define monoclinic @7 @8 @9 90.0 60.0 90.0
crystal build cutoff 15.0

............

But the program can't run, and if I delete the line "crystal build....", it becomes to run, but I am not sure my molecule moves just in the box, not outside the box.
So, what's wrong with my input file?
Thank you very much!!

hauren32

Re: one problem about box setting
hauren32 #5739 03/09/05 07:21 AM
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Everything is wrong. This will not work as intended. The crystal and image facilities are only for PBC simulations, and cannot be used to implement a hard-wall box.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: one problem about box setting
hauren32 #5740 03/09/05 08:45 AM
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Dear sir,
Thank you for your reply.
As you mention, my setting is just for PBC, but if I want to set the hard-wall box, how should I do? or can charmm program do it?
Thank you very much~

hauren32

Re: one problem about box setting
hauren32 #5741 03/09/05 08:59 AM
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you best bet is probably to construct physical walls using very hard L-J spheres (non-charged) constrained on a grid; this is not a all difficult to do.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: one problem about box setting
hauren32 #5742 03/09/05 09:20 AM
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Dear sir,
Thank you very much!
But could you tell more clearly? Is there any charmm document for me? or some example? I don't have any experience about this.

hauren32

Re: one problem about box setting
hauren32 #5743 03/09/05 09:55 AM
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This is really very simple, but sligthly tedious, and I cannot do it for you.
The basic steps are to create a residue (in your favorite RTF) containing just one non-charged (carbon) atom and then to generate a segment with as many such residues as you need to build a wall. Coordinates can be generated manually, or with a simple program, or even inside CHARMM using a loop. Finally you may want to play with the parameters (in the parameter file) for the size (Rmin) and attractive potential depth (epsilon) of the atoms that make up your wall.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: one problem about box setting
lennart #5744 03/09/05 01:10 PM
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Daer sir,
Sorry, sir. Although you told very clearly, I was still confused. I don't know why I have to create a residue containing just one carbon atom, and the wall as if a carbon wall? Is there no any other method? Actually, I don't know how to deal with my work, I just want to set a monoclinic box with its length, 130x250x130, and angles, 90,60,90.
Thanks a lot!!

hauren32

Re: one problem about box setting
hauren32 #5745 03/09/05 02:44 PM
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You do not have to have just one atom per residue and it does not have to be a carbon atom, all I suggest is that you construct physical walls of immovable particles that mainly provide a repulsive interaction to keep your system confined within the volume of interest.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: one problem about box setting
hauren32 #5746 03/09/05 05:44 PM
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First, it's not clear at all why you would wish to do this, or at least why you don't use a large cubic box. A monoclinic lattice is most often used for crystals with P21 symmetry. Exactly what are you trying to do, and why?

The very short cutoff for CRYSTAL BUILD may a problem at the very least-- it should probably be more like half the longest cell dimension, esp. if there's considerable vacuum space inside the volume.

Try posting the last page or so of the output with some error messages; "the program can't run" doesn't provide any useful information.


Rick Venable
computational chemist

Re: one problem about box setting
rmv #5747 03/09/05 10:58 PM
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So this would suggest a "crystal build cutoff 150 noper" in this case?

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