[AMBER] Serious problem at specific time point

From: Hoshin Kim <85hskim.gmail.com>
Date: Wed, 10 Nov 2010 17:39:34 +0900

Dear Amber user,

I'm trying to do simulation about Enzyme in various solvents, using AMBER11.
But I have a serious problem on my trajectory.
When I calculated RMSd of catalytic domain of enzyme, slope was suddenly
soared at 4.8ns (I attached a plotting data). So I ran the VMD to visualize
what happened at this point, as I attached, protein structure was suddenly
collapsed at that point !
This is my second try. This problem was occurred at almost same point when I
tried to do first simulation using same enzyme, same protocol. So I think
this error is not the cause of hardware, or something like that
I'm doing one more simulation using different solvent, It has also same
problem. (Peak is suddenly increased at specific time-steps) only difference
is time point.

Could anyone figure out this serious problem?

Thanks in advance,

Hoshin Kim,


1.Attached files are only about the problem which I explained first.
2.First case, solvent is 0.3M NaCl solution, Second case, [Bmim][TfO]
3.I am using enzyme named 1TCA (CalB), and protocol for production MD is as
   ntxo=1, ntrx=1,
   cut=9.0, tempi=300.0, ntwprt=0,
   ntpr=500, ntwx=500, ntwe=500, ntwr=500,
   nstlim=10000000, temp0=300.0,
   dt=0.002, nscm=100,nsnb=10,dielc=1.0,
   ntc=2, ntf=2, tol=0.00001,
   ntx=5, irest=1, heat=0.0,
   ntb=2, ntp=1, pres0=1.0, taup=0.5,
   scee=1.2, dt=0.002,
   ntt=1, vlimit=20.0,comp=44.6,
If further protocols are need to figure out this problem (Protocols for
minimization, equilibration ...), please tell me !

Hoshin Kim
Visiting Scholar
Department of Chemical and Biomolecular Engineering
North Carolina State University
Raleigh, NC 27695
Phone: 919-986-9258
Graduate student (M.D. candidate)
Ionic Liquids Team(ILs) in Bio Nano Process Lab
Department of Biological Engineering,
2S 113, Engineering building Inha University,
253 Yonghyeon Dong, Nam Ku
Incheon, KOREA
TEL) +82-32-860-8655

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Received on Wed Nov 10 2010 - 15:00:03 PST
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