AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Feb 23 2009 - 06:08:07 CST

correct, unless you change use_pme, it will default to on.
try removing the entire &ewald section, that's not needed unless you
want to change defaults, and you may have other typos there. you can
try to add it back if it works without it. look carefully for error
messages in any other output, such as error files from the queueing
software.

On Mon, Feb 23, 2009 at 7:03 AM, parul sharma <sharmaparul7373_at_gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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