VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Mon Sep 19 2005 - 15:08:15 CDT

On Mon, 19 Sep 2005, John Stone wrote:

>
> Hi,
> If you've lost molecules to the far reaches of empty space and
> the simulation isn't using periodic boundary conditions, then you're
> just going to have to scale down the molecule and crank up the
> far clip plane to something large. Try reducing the size by 10:
> scale by 0.1

Thank you, John. This was the case. Please tell me how to do "scale by
0.1". Thank you.
Sincerely,
Margaret

> On Sun, Sep 18, 2005 at 04:11:45PM -0400, Margaret Shun Cheung wrote:
>> Dear VMD wizards,
>>
>> I had a md simulations and molecules slowly drifted away, disappeard from
>> the screen. I tried to adjust Near clip to 0 and far clip to 30, but
>> still can't prevent such trajedy.... Please help. Thank you.
>>
>>
>> Margaret S. Cheung,
>> Ph. D. Postdoctoral Fellow,
>>
>> ------------------------------------------------------------
>> Room 2117 Tel: (301) 405-4892
>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>> University of Maryland http://glue.umd.edu/~mscheung
>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>> ------------------------------------------------------------
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>

Margaret S. Cheung,
Ph. D. Postdoctoral Fellow,

------------------------------------------------------------
Room 2117 Tel: (301) 405-4892
Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
University of Maryland http://glue.umd.edu/~mscheung
College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
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