In my experience, it will. It was a problem a long time ago, but now it
seems it was solved. I'm mostly using ntx = 5 since I'm doing more GB
calculations now. But I believe ntx = 7 should be fine. I used to always
manually modify the sizes in parm file after belly dynamics. Now I don't.
However, checking the output won't hurt.
Guanglei Cui
-----Original Message-----
From: Jake Isaacs [mailto:rjisaa0_at_pop.uky.edu]
Sent: Friday, February 16, 2001 1:54 PM
To: AMBER list
Subject: Re: periodic box size
Does this mean box sizes in the restrt file will _always_ override those in
prmtop, or only when ntx=6 or 7?
>Hi,
> In amber6, the box information from restart files will override A, B,
>and C in your input file. The box information specified in your input file
>will override that of parm file. If you're using older version, I remember
>the box size should be better dividable by 2, 3 or 5 to make the
calculation
>faster. The larger the box size, more time is needed. Perhaps it's
automatic
>in amber6 now.
>
>Regards,
>
>Guanglei Cui
>
>-----Original Message-----
>From: Raja Swaminathan [mailto:rajaamber6_at_rediffmail.com]
>Sent: Friday, February 16, 2001 12:25 PM
>To: amber_at_cgl.ucsf.edu
>Subject: periodic box size
>
>
>hi amber users
>i have done md simulations on a 14 mer DNA duplex.
>the box size is
>
>42.7539974 43.0651857 45.8525446
>
>i have used the next line as 43 43 46
>
>will it be there any problem in md simulations or
>the system will take only more computational time.
>
>thanks
>
>raja
>
>_____________________________________________________
>Chat with your friends as soon as they come online. Get Rediff Bol at
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>
>
>
>
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Received on Fri Feb 16 2001 - 11:48:50 PST
