AMBER Archive (2005)

Subject: Re: AMBER: (no subject)

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Tue Sep 27 2005 - 06:06:16 CDT

I think that you need nmropt=1 to read the weight
changes, and you also must include&rst file info . Check the
manual for examples.

Andrew Box wrote:

> Dear All
>
> I am trying to run a MD simulation where the temperature increases
> over the run from 0k to 300K. To do this i am using the &wt function
> in the .in file. The input file is as follows:
>
> polyA-polyT 10-mer: 5ps MD with res on DNA with heating from 100K to
> 300K, DNA
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 10,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> ntt = 1, tautp=0.2
> nstlim = 500,
> ntpr = 100, ntwx = 2500, ntwr = 1000
> /
>
> &wt type='TEMP0', istep1=0,istep2=200,value1=100.0, value2=150.0, /
> &wt type='TEMP0', istep1=201, istep2=300, value1=150.0,
> value2=200.0, /
> &wt type='TEMP0', istep1=301, istep2=400, value1=200.0,
> value2=250.0, /
> &wt type='TEMP0', istep1=401, istep2=500, value1=250.0,
> value2=300.0, /
>
> &wt type='END' /
> Hold the DNA fixed
> 10.0
> RES 1 23
> END
> END
>
>
> The run fails. When iu check the output file i get the following
> error message:
>
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
>
>
> rfree: Error decoding variable 1 3 from:
> &wt
>
> this indicates that your input contains
>
> incorrect information
>
> field 1 was supposed to
>
> have a (1=character, 2=integer, 3=decimal) value
>
>
> When I deleted all the &wt lines, the run works fine. Any help would
> be greatly appreciated.
>
> Andrew Box
>
> _________________________________________________________________
> REALESTATE: biggest buy/rent/share listings
> http://ninemsn.realestate.com.au
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor           Phone: (631) 632-1336
Center for Structural Biology Fax:   (631) 632-1555
Stony Brook University        Web:   http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115    E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

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