Update your AMBER installation - latest should be v12.3. - This may be
related to a bug fixed by bugfix.18. It is also possible that your
structure is not well behaved- it is also possible that since you are not
running shake that a 1fs time step is too long for stability. Cut it to
0.5fs and that might help.
I assume you are using a flexible water model here. Things like TIP3P do
NOT work without shake.
All the best
Ross
On 8/20/13 9:13 AM, "WuYunjian" <yunjian.wu.hotmail.com> wrote:
>
>
>
>Dear All,
> I am running a globular protein simulation in explicit water
>box. The version information is
>--------------------- INFORMATION ----------------------| GPU (CUDA)
>Version of PMEMD in use: NVIDIA GPU IN USE.| Version
>12.2|| 01/10/2013
>The input script :
>production &cntrl imin=0, irest=1, ntx=5, ntb=2, pres0=1.0, ntp=1,
>taup=2.0, cut=12.0, ntr=0, tempi=300.0, temp0=300.0, ntt=3,
>gamma_ln=1.0, ioutfm=1, ntxo=2, nstlim=20000000, dt=0.001, ntpr=5000,
>ntwx=5000, ntwr=5000 /
>When the simulation run to 325000 steps. The out file was written like
>this:
>NSTEP = 325000 TIME(PS) = 1225.000 TEMP(K) =********* PRESS
>=236279.7 Etot = ************** EKtot = ************** EPtot =
>************** BOND = -0.0000 ANGLE = 412443.8176 DIHED
> = 12858.2191 1-4 NB = 0.0000 1-4 EEL = 0.0020
>VDWAALS = ************** EELEC = 240774.4654 EHBOND =
>0.0000 RESTRAINT = 0.0000 EKCMT = -0.0000 VIRIAL =
>-2600947.1897 VOLUME = 509832.1771
> Density = 0.5858
>--------------------------------------------------------------------------
>----
>And then, it stopped with this error:
>| ERROR: max pairlist cutoff must be less than unit cell max sphere
>radius!
>How could I fix this problem ?
>Thank you very much.
>
>
>
>
>
>
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Received on Tue Aug 20 2013 - 12:00:03 PDT
