AMBER Archive (2009)

Subject: Re: [AMBER] PME doesn't work

From: parul sharma (sharmaparul7373_at_gmail.com)
Date: Mon Feb 23 2009 - 06:03:54 CST

Dear Carlos,

Thanks for your reply. Yes, the job stops after giving this flag message. I
again tried with the comma but still not working, the job is not proceeding
further.

Also if i run my job under NVT or NPT, that means i am applying PME because
in the Amber manual it syas PME is alwayz ON if ntb > 0 ?

On Mon, Feb 23, 2009 at 1:19 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> there is no problem with the part you quoted, and it is not an error
> message. please tell us why you think PME doesn't work.does the job
> stop after this part?
>
> it does appear that you are missing a comma in your input before
> nfft1. it can be helpful to
> try not having &ewald section and see if that works. you can often
> troubleshoot input problems by deleting sections or keywords from your
> input and trying again. this helps you find typos, etc.
>
> are you sure you need to specify these things, such as a b c etc?
>
>
> On Mon, Feb 23, 2009 at 4:43 AM, parul sharma <sharmaparul7373_at_gmail.com>
> wrote:
> > Dear All,
> >
> > I did MD simulation with NVT for 100 ps, and then i proceeded with NPT,
> > but when i try to include PME (the input for which is given below)
> >
> > &cntrl
> > imin = 0, irest = 1, ntx = 7, ntb = 2, ntp = 1, pres0 = 1.0, taup = 2,
> > cut = 10, tempi = 300.0, temp0 = 300.0,
> > ntc=2, ntf=2, tol = 0.0001,
> > ntt = 3, gamma_ln = 1.0,
> > scee= 1.2, nstlim =250000, dt = 0.002,
> > ntpr = 500, ntwx = 500, ntwr = 500, ntwe = 500,
> > &ewald
> > ew_type = 0 nfft1 = 25, nfft2 = 25, nfft3 = 20,
> > a = 58.8103873, b = 47.4014584, c = 33.2335295,
> > alpha = 90.0, beta = 90.0, gamma = 90.0
> > order = 4, dsum_tol = 0.00001,
> > /
> >
> > It gives me the following error in the output:
> >
> > | Flags: MPI
> > getting new box info from bottom of inpcrd
> > | INFO: Old style inpcrd file read
> > | peek_ewald_inpcrd: Box info found
> >
> > Can anyone please help me in sorting the problem out?
> >
> > --
> > With Best Regards
> >
> > Parul Sharma
> > PhD Student, Durban University of Technology,
> > Durban,
> > South Africa
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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> 

-- 
With Best Regards

Parul Sharma
PhD Student, Durban University of Technology,
Durban,
South Africa
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