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 - 05:30:04 PDT
