AMBER Archive (2004)

Subject: Re: AMBER: non-periodic simulation and box information !!

From: Michael Crowley (crowley_at_scripps.edu)
Date: Wed Apr 21 2004 - 12:32:58 CDT

Dear Pradipta,
The default for ntb is 1, periodic constant-volume simulations.
That is why sander is looking for box information.
Your simulation is not nonperiodic from the content of your mdin.
If you want nonperiodic, you need to specify ntb=0.
Mike

-----------------------------------------------------------------
Physical mail: Dr. Michael F. Crowley
                 Department of Molecular Biology, TPC6
                 The Scripps Research Institute
                 10550 North Torrey Pines Road
                 La Jolla, California 92037

Electronic mail: crowley_at_scripps.edu
Telephone: 858/784-9290
Fax: 858/784-8688
-----------------------------------------------------------------

On Wed, 21 Apr 2004, Pradipta Bandyopadhyay wrote:

> Hi,
>
> It seems that Sander needs box information even
> for the non-periodic simulation for both minimization
> and dynamics. Is it true?
>
> My input file for minimization is:
>
> &cntrl
> IMIN=1,
> NTMIN=1,
> NCYC=100,
> maxcyc=1000,
> &end
>
> and if I don't put box information in the .top
> file the output file error is:
>
> | peek_ewald_inpcrd: Box info not found in inpcrd
> compute_nfft: failed to get good fft array size
> x = 1.68611748111448396E+69
>
> It seems ewald tried to read the box information.
>
> However, if I put the box information (setBox in leap)
> it is fine and for the dynamics it is doing
> non-periodic simulation.
>
> Pradipta
>
>
>
>
>
>
> ==============================================
>
> This Mail was Scanned for Virus and found Virus free
>
> ==============================================
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu