On Tue, Mar 9, 2010 at 6:02 PM, Amire-Brahimi Benjamin
<bxa8300.louisiana.edu> wrote:
> So I tried with the irestrt = 1 and ntx = 5 like you have stated but I still
> get the same error.
>
> FATAL: Could not read velocities from min_chaina_gol.crd
This means that min_chaina_gol.crd does not have any velocities. This
is easy to check. If it does have velocities, then there will be 6
times as many numbers in that file as there are atoms (3 for each
position and 3 for each atom's velocity). There will be an additional
3 if there is box information. If there is no velocity information,
then use irest=0, ntx=1.
Good luck!
Jason
>
> This is my command line to restart the MD simulation
>
> /home/packages/amber/10/intel-11.1-mvapich-1.1/bin/sander -O -i
> complexmdrest.in -o complexmdrest.out -p min_chaina_gol.top -c
> min_chaina_gol.crd -r md1.rst -x chaina_min_mdcrd1.mdcrd -v
> chaina_mdvel1.mdvel -inf chaina_mdinfo1.mdinfo
>
> Here is my input file:
> Restart simulation
> &cntrl
> imin = 0,
> ntx = 5,
> irest = 1,
> ntrx = 1,
> ntxo = 1,
> ntpr = 50,
> ntwx = 1000,
> ntwv = -1,
> ioutfm = 1,
> ntwe = 1000,
> ntwr = 1000,
> ntf = 2,
> ntb = 2,
> ntp = 1,
> pres0 = 1.0,
> cut = 10.0,
> nsnb = 20,
> ibelly = 0,
> ntr = 0,
> imin = 0,
> nstlim = 2500000,
> nscm = 500,
> t = 0.0,
> dt = 0.002,
> temp0 = 298.0,
> tempi = 298.0,
> ntt = 1,
> vrand = 0,
> vlimit = 15.0,
> ntc = 2,
> &end
>
> Thanks,
>
> Ben
>
> --
>
>
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Mar 09 2010 - 15:30:03 PST
