Hi Yang,
I am also not sure if your time step dt = 0.01 is the lucky one.
Usually you need dt = 0.002 (with hydrogen constraint (SHAKE)) or dt =
0.001 (without hydrogens constrained ).
Best,
Marek
Dne Tue, 30 Mar 2010 03:40:41 +0200 Yang Li <chlorin316.hotmail.com>
napsal/-a:
>
> Hi,
> I took Dr. Case's recommendation and run a 10 step simulation. The test
> case did not pass, it was running and I tried to tail -f the .out file,
> but nothing showed up. The simulation ran for the entire weekend and
> there's no output file so I stopped it.
> What do you think the problem is?
>
>
> With regards,
> Yang
>
>> From: carlos.simmerling.gmail.com
>> Date: Mon, 29 Mar 2010 15:58:40 -0400
>> Subject: Re: [AMBER] simulation under pressure
>> To: amber.ambermd.org
>>
>> have the test cases passed? is the job still getting CPU time? do you
>> get
>> any output at all?
>>
>> On Mon, Mar 29, 2010 at 3:53 PM, Yang Li <chlorin316.hotmail.com> wrote:
>>
>> >
>> > Hi, Dr. Case,
>> >
>> > Thank you for you recommendations. I checked and my prmtop was
>> > periodic and solvated. I tried to run a 10 step simulation, here is my
>> > input file.
>> >
>> > DNA 12-ATmer simulation under 100atm
>> > &cntrl
>> > imin = 0, irest = 1,
>> > igb = 0, ntx = 5,
>> > ntt = 3, gamma_ln = 1.0,
>> > tempi = 300.0, temp0 = 300.0
>> > ntp = 1, taup = 2.0, pres0 = 100,
>> > ntb = 2, ntc = 2, ntf =2,
>> > nstlim = 10, dt = 0.01
>> > ntwx = 1, ntpr =1
>> > cut = 12.0
>> > /
>> >
>> >
>> > However, the simulation has run for the entire weekend again and did
>> > not finish on the 3G processor.
>> >
>> > Please let me know what I can do.
>> >
>> >
>> > With regards,
>> >
>> > Yang
>> > _________________________________________________________________
>> > Check your Hotmail from your phone.
>> >
>> >
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Received on Tue Mar 30 2010 - 03:30:03 PDT
