Dear Prof.case
Thanks a lot for your comments. There is a metal ion in my protein sysytem.It tetracoordinated to three residues as well as one water molecule.The number 9223 and 9224 is the H atom in the water molecule which bonded to the metal ion. I used the bonded model in Amber. The parrel simulation runs well during the heating process,but when I run the MD in the NPT,the error happens.My input file is :
&cntrl
imin=0,irest=1,ntx=5,
ntb=2,pres0=1.0,ntp=1.0,taup=2.0,
cut=8.0,ntr=0,
ntc=2,ntf=2,
tempi=300.0,temp0=300.0,
ntt=3,gamma_ln=1.0,
nstlim=500000,dt=0.002,
ntpr=500,ntwx=500,ntwr=1000
/
your comments are highly appreciate!
At 2010-10-11 19:40:30，case <case.biomaps.rutgers.edu> wrote:
>On Mon, Oct 11, 2010, xuemeiwang1103 wrote:
>
>> partition error in shake on processor.
>> this processor has atoms 9224 through 11195
>> atom 9224 is within this range
>> atom 9223 is not witnin this range !
>
>Is there anything non-standard about your system, i.e. other than just a
>pure protein? Did you create any cross-links? Sander assigns atoms to
>processors in a way that no bonds to hydrogen go across boundaries, but
>this seems to have failed in your case. What are atoms 9223 and 9224?
>What value of ntc have you used?
>
>I don't recall seeing this problem before, so you may have to post your files
>to provide more details.
>
>....dac
>
>
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Received on Mon Oct 11 2010 - 19:00:02 PDT
