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

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Mon, 12 Apr 2010 07:09:45 -0400

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
interval, not the same # frames? 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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> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Apr 12 2010 - 04:30:03 PDT
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