Dear Youyi Peng:
It's posible that you found the same problem that I did! Is your
trajectory file very large? Over 2 Gb? Was it complete (I mean did
sander completed all the requested steps?)?
Try running the simulation redirecting the standart output to a file
(sander ... bla, bla, bla >& >errorfile.out for example).
If so, you either divide your simulation in several parts or decress the
frequency of writting to the traj file!
Hope it helps!
Sincerely
Marco A. C. Preto (Ph. D. student)
Theoretical Chemistry goup
Chemistry Depart. - FCUP
Porto, Portugal
Youyi Peng wrote:
> Dear Amber users:
> I ran a 100ps MD two times. During MD running, the energy summaries
> were output to the output file. I checked the output file with 'more'
> and 'tail'. After the MD finished, the summaries were gone in the output
> file. There is no any output in the .out file. BUt the restrt and mdcrd
> files were both output normally. The mdin file worked correctly for
> previous MD run. What caused the problem?
> Thanks! -----Youyi
>
> This is the input file:
> &cntrl
> nmropt = 0,
> ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
> ntpr = 1000, ntwx = 1000, ntwv = 0, ntwe = 0,
>
> ntf = 1, ntb = 0,
> cut = 13.0, nsnb = 10, dielc=4.0
>
> ibelly = 0, ntr = 0,
>
> imin = 0,
> nstlim = 100000,
> nscm = 500,
> dt = 0.001,
>
> temp0 = 300.0, tempi = 300.0,
> heat = 0.0,
> ntt = 1,
> tautp = 2.0,
> vlimit = 20.0,
>
>
> ntc = 1, tol = 0.00001,
> &end
>
> &ewald
> eedmeth=5,
> &end
>
>
Received on Tue May 13 2003 - 09:53:00 PDT
