Re: [AMBER] Restart Problem: The results of an integrated simulation and restarted simulations are not equal!

From: Ali M. Naserian-Nik <>
Date: Tue, 1 Mar 2011 12:12:52 +0330

Dear Prof. Case,

Thank you very much for your comments. I think the structural differences at
the end of the two test simulations are not negligible (I attach the
corresponding PDB files). Is there any way to reduce the errors as much as
Also here is my input file:

   imin=0, ntx=7, irest=1, ntb=0,
   ntc=2, ntf=2,
   cut=150, igb=1, extdiel=79, saltcon=0.13, gbsa=1,
   ntpr=100, ntwx=100, ntwr=10,
   tempi=300.0, temp0=300.0, ntt=3, gamma_ln=3, ig=-1,
   nstlim=40000, dt=0.001,

On Mon, Feb 28, 2011 at 10:26 PM, case <> wrote:

> On Mon, Feb 28, 2011, Ali M. Naserian-Nik wrote:
> >
> > To find out if splitting a long simulation to some shorter simulations
> with
> > the aid of “irest=1” option, I performed two 40 ps test run for a DNA
> > dodecamer: 1) 40 ps integrated simulation and 2) 20 + 20 ps successive
> runs
> > (the 2nd 20 ps simulation was started y restart option “ntx=7” just after
> > the 1st 20 ps simulation). When I compared the resulting RMSD curves of
> the
> > backbone and also PDB files obtained at the end of the two 40 ps
> > simulations, I found that unexpectedly they are not the same!
> This is to be expected, depending somewhat on *how* different the two
> results
> are. There is some truncation of precision with a restart file, and hence
> some small initial deviations that eventually grow and dominate the
> results.
> Please see section 1.3.4 of the Amber11 Users' Manual.
> If you want to see for yourself what is going on, compare 40 *steps* of MD
> (not 40 ps), setting ntpr=1, and then restart in the middle.
> This, of course, is a repeat of my usual hobby-horse of suggesting the
> virtues
> of short runs with ntpr=1 when problems or questions arise about what is
> going
> on in MD simulations.
> ....dac
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Received on Tue Mar 01 2011 - 01:00:04 PST
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