Hi Ross,
Thanks for your reply. I will try to fix it according your suggestion.
Regards.
Yunjian WuPh.D. CandidateState Key Lab of Theoretical & Computational ChemistryInstitute of Theoretical ChemistryJilin UniversityChangchun, 130023P.R. China
> Date: Tue, 20 Aug 2013 11:30:51 -0700
> From: ross.rosswalker.co.uk
> To: amber.ambermd.org
> Subject: Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius
>
> 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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>
>
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Received on Wed Aug 21 2013 - 08:00:02 PDT
