AMBER Archive (2005)

Subject: Re: AMBER: SHAKE error

From: David A. Case (case_at_scripps.edu)
Date: Fri Jul 22 2005 - 11:04:15 CDT

On Fri, Jul 22, 2005, Agata Jurkiewicz wrote:
>
> It goes about 12-17 ps (depending on the size of waterbox) and fails
> with a message:
> [from md.out file:]
>
> NSTEP = 6300 TIME(PS) = 62.600 TEMP(K) = 479.96 PRESS = 1029.9
> Etot = -3922.0613 EKtot = 2086.3751 EPtot = -6008.4364
> BOND = 8.2350 ANGLE = 16.6152 DIHED = 17.7050
> 1-4 NB = 7.1684 1-4 EEL = -107.8100 VDWAALS = 817.9307
> EELEC = -6768.2806 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 1007.0906 VIRIAL = 403.0253 VOLUME = 27165.7778
> Density = 0.8072
> Ewald error estimate: 0.1265E-02
>
> vlimit exceeded for step 6301 ; vmax = 103.896044101908
>

Let me add to what Carlos said: you have a big step size (0.002) and still
a low density (0.8) but a high temperature (480K). This can readily lead
to SHAKE failures.

A good prescription is to heat to a stable 300K at constant volume, then
switch to constant pressure, not allowing the temperature to rise very much
when you do that. It is not all that uncommon for equilibrations to require
shorter time steps (like .001), and smaller values for tautp.

...good luck....dac

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