Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?

From: Jianing <song_jianing_hi.126.com>
Date: Mon, 12 Apr 2010 20:37:30 +0800 (CST)

when the coordinates are saved every 4fs, the program sander just exits automatically at 3.5ns for the dynamic run. and the XRD structure bacomes unstable at 2ns. The time is not very long, so this also surprises me. I change to pmemd and get the same results.
you may say there is something wrong with my operation, and the following is my executing file to demenstrate that the whole process is proceeded by computer automatically, and I don't change anything during the simulation.

run.sh:

for i in `seq 1 500`

do

let "j=i-1"

mpirun -n 8 pmemd -O -i md.in -o md${i}.out -p vilppcxrd.prm -c md${j}.rst -r md${i}.rst -x md${i}.mdcrd </dev/null

echo "

trajin md${i}.mdcrd

trajout md${i}.dcd charmm " > p.in

ptraj vilppcxrd.prm p.in

rm p.in

rm md${i}.mdcrd

done

what I just have done is prepare the input file md.in and the initial parmtop file and coordinates file vilppcxrd.prm and md0.rst.

Thanks

Jianing

 






2010-04-12 20:13:31"Carlos Simmerling" <carlos.simmerling.gmail.com> д
>no- what I meant is what is the length of simulation you are comparing? how
>long before the XRD structure becomes unstable?
>
>2010/4/12 Jianing <song_jianing_hi.126.com>
>
>> Thank you very much for your reply.
>> yes, I'm sure using the same Amber binary, the same machine, the same
>> number of CPU and comparing the same time interval. The results shock me, so
>> I have checked everything that may affect the simulation.
>>
>>
>> >writing every 4fs is very often, and would
>> >probably give very laerge output files for a simulatino long enough to
>> lose
>> >the XRD structure
>>
>> what is the extrat meaning of this? Do you mean that writing the
>> coordinates too often is equil to run MD simulation for a long time that may
>> cause to lose XRD structure.
>>
>> Thanks in advance.
>>
>> Jianing
>>
>>
>>
>> 2010-04-12 19:09:45"Carlos Simmerling" <carlos.simmerling.gmail.com> д
>> >the frequency of saving does not change the simulation. Are you sure that
>> >you ran them using the same Amber binary, on the same machine, using the
>> >same # of CPus, etc? many things can cause trajectories to diverge. Have
>> you
>> >diffed the mndout files? are you sure that you are comparing the same time
>> >writing every 4fs is very often, and would
>> >probably give very laerge output files for a simulatino long enough to
>> lose
>> >the XRD structure.
>> >
>> >2010/4/12 Nancy <song_jianing_hi.126.com>
>> >
>> >> Dear all,
>> >>
>> >> Recently I'm involved in performing MD simulation using AMBER.
>> >> At the beginning, the atom coordinates are saved to mdcrd file in every
>> >> 4fs(ntrw=2) time interval. Then for comparison, I save the atom
>> coordinates
>> >> into mdcrd file every 10ps(ntrw=5000). Other parts of the two MD
>> simulations
>> >> are all the same, and the only difference is the frequency of saving
>> atom
>> >> coordinates. But the conformation between the two simulation give huge
>> >> difference. That from former protocol is far from the XRD structure at
>> the
>> >> end. But that from the latter is similar to the XRD structure.
>> >>
>> >> This results shocks me, because the frequency of saving atom coordinates
>> >> shouldn't affect to MD simuation. I've checked all the input files, they
>> are
>> >> the same, except options controlling the output such as 'ntwx'. The
>> program
>> >> I use is sander in AMBER10, AMBER03 is the force field by which I've
>> adopted
>> >> to perform simulation. My system is villin headpiece. Furthermore,
>> explicit
>> >> solvation model TIP3P is used.
>> >>
>> >> The following is the two input file:
>> >>
>> >> ---The frequently-output input-------------
>> >> &cntrl
>> >> imin = 0,
>> >> irest = 1,
>> >> ntx = 5,
>> >> ntb = 1,
>> >> cut = 12.0,
>> >> ntc = 2,
>> >> ntf = 2,
>> >> tempi = 300.0,
>> >> temp0 = 300.0,
>> >> ntt = 3,
>> >> gamma_ln = 1.0,
>> >> nstlim = 5000, dt = 0.002
>> >> ntpr = 2, ntwx = 2, ntwr = 2
>> >> /
>> >> ----------------------------------------
>> >> ---The not-so-frequently-output input---
>> >> &cntrl
>> >> imin = 0,
>> >> irest = 1,
>> >> ntx = 5,
>> >> ntb = 1,
>> >> cut = 12.0,
>> >> ntc = 2,
>> >> ntf = 2,
>> >> tempi = 300.0,
>> >> temp0 = 300.0,
>> >> ntt = 3,
>> >> gamma_ln = 1.0,
>> >> nstlim = 2500000, dt = 0.002
>> >> ntpr = 5000, ntwx =5000 , ntwr = 5000
>> >> /
>> >> ----------------------------------------
>> >> can someone give me some advice and help me out of the trouble?
>> >> Thank you very much in advance.
>> >> Jianing
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Received on Mon Apr 12 2010 - 06:00:09 PDT
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