On Fri, Apr 20, 2018, Ashutosh Shandilya wrote:
>
> I ran MD simulation for 10 ns and then tried to run aMD with following
> parameters
> ---------------------------------------------------------
> Accelerated MD - explicit solvent
> &cntrl
> imin=0, irest=0, ntx=1, nstlim=25000000, dt=0.002, iwrap=1,
> ntb=2, cut=10.0, ntp=1, ntc=2, ntf=2, tempi=300.0, temp0=300.0,
> ioutfm=1, ntt=3, gamma_ln=1.0, ig=-1, iamd=1,
> EthreshP=-152417, alphaP=13330, barostat=2, ntpr=5000, ntwr=5000,
> ntwx=5000
> &end
> -------------------------------------------------------------------------
>
> I encountered with this error while running aMD.
I'm lost here: what exactly is the error you encountered?
>
> Although, I am not sure why aMD output file shows higher temperature at the
> first step
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = *437.64*
If this is the error you are referring to, you should ignore it. You
set irest=0, and re-sampled velocities from a Maxwell-Boltzmann
distribution at tempi=300K. However, the reassignment procedure used
does not correctly account for SHAKE constraints, so the first step
temperature will be wrong. It will very quickly come back to temp0.
The easiest thing to do is to set irest=1 and ntx=5. If you indeed wish
to resample velocities, and are unhappy with the first temperature, you
can use cpptraj to create new velocities in the restart file, and then
use the modified file (still with irest=1).
...good luck....dac
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Received on Sat Apr 21 2018 - 06:30:03 PDT
