have you diffed the mdout files?
2010/4/12 Jianing <song_jianing_hi.126.com>
> 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
>
>
>
>
>
>
>
>
> 在2010-04-12 20:13:31，"Carlos Simmerling" <carlos.simmerling.gmail.com> 写道：
> >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
> >>
> >>
> >>
> >> 在2010-04-12 19:09:45，"Carlos Simmerling" <carlos.simmerling.gmail.com>
> 写道：
> >> >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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> >> >>
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Received on Mon Apr 12 2010 - 07:30:04 PDT
