Re: AMBER: references

From: Ricardo J. F. Branco <ricardo.branco.fc.up.pt>
Date: Fri, 23 Jun 2006 11:47:50 +0100

Dear Simon,

You could define periodic boundary conditions using the flag NTB, like in the
following script:

&cntrl
        ntx=7,iwrap=1,irest=1,
        ntpr=100,ntwx=500,ntwr=-100000,
        nstlim=500000,dt=0.001,
        ntf=2,ntc=2,ntb=2,tol=0.00000001,
        temp0=300.0,ntt=1,tautp=1.0,
        pres0=1.0,ntp=1,taup=1.2,
&end

Cheers,

RB


Quoting simon whitehead <sjw084.bham.ac.uk>:

> Dear Amber users,
>
> Please could someone tell me the correct reference to use for PME and
> for the use of periodic boundaries in amber 8?
>
> Many thanks
>
> simon
>
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-- 
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Ricardo J. F. Branco, Ph.D. Student
Theoretical and Computational Chemistry Group
REQUIMTE - Faculty of Science
University of Oporto
Rua do Campo Alegre, 687
P 4169-007 Porto, Portugal
e-mail: ricardo.branco.fc.up.pt
Phone: (+351) 226 082 826
Fax:   (+351) 226 082 959
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Received on Sun Jun 25 2006 - 06:07:18 PDT
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