Re: AMBER: problem with ptraj and randomizeions

From: Filip Lankas <>
Date: Fri, 18 Feb 2005 13:19:10 +0100

Hello Fabien,

and if you type just one command randomizing everything at once, say

randomizeions :437-yourmaxion around :1-436 by 5.0 overlap 3.5

does it work then?

We have noticed yet another kind of behaviour (using the mask scheme
above) - sometimes the randomized ions are not distributed uniformly at
all but somehow accumulate in one corner of the box - and it doesn't get
better when we randomize several times in a row. Of course this may be a
matter of statistics but it seems so unlikely, doesn't it? We checked
that the mask contains all the ions and nothing else.



Fabien Cailliez wrote:
> Dear Dr Cheatham,
> I am using ptraj-6.5 version.
> The problem is for a K+ ion (not the first and not the last) which is
> displaced but not as far from the solute as I would
> like to. In the output of ptraj, I can see that all the ions I put in
> the mask were understood by ptraj.
> Everything looks fine during ptraj works and I never had this problem
> before although I used this command
> many times...
> I also checked at the mask using rdparm and everything is OK.
> As there is only one K+ incorrect, it is simple to randomize once again
> only this ion and now everything is fine, but
> but this problem is a bit worrying.
> Fabien

Dr. Filip Lankas
Institute for Mathematics B
EPFL (Swiss Federal Institute of Technology)
Station 8
CH-1015 Lausanne
Tel: +41 21 693 2593    Fax: +41 21 693 5530
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Received on Fri Feb 18 2005 - 12:53:00 PST
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