Dear Prof.Carlos Simmerling ,
Great thanks for your kind help!
Best regards
On 4/29/06, Carlos Simmerling <carlos.csb.sunysb.edu> wrote:
>
> you should sue sander.MPI. even though you only use
> a single CPU it still needs the parallel version of sander.
>
> pang zhao wrote:
>
> > Sorry, I use the amber 9 not the amber 8 to perform remd. Now, I
> > revised my email:
> >
> > I use sander module of amber 9 to perform replica exchange MD. I just
> > use 4 replicas to have a try. I just use single cpu to do it.
> > My commands:
> >
> > sander -ng 4 -rem 1 -remlog remd.log -groupfile group &
> >
> > the conten of file group:
> > -O -i mdin.rep1 -o mdout.rep1 -c min.restrt -p 1.prmtop -r re.rep1 -x
> > mdcrd.rep1
> > -O -i mdin.rep2 -o mdout.rep2 -c min.restrt -p 1.prmtop -r re.rep2 -x
> > mdcrd.rep2
> > -O -i mdin.rep3 -o mdout.rep3 -c min.restrt -p 1.prmtop -r re.rep3 -x
> > mdcrd.rep3
> > -O -i mdin.rep4 -o mdout.rep4 -c min.restrt -p 1.prmtop -r re.rep4 -x
> > mdcrd.rep4
> >
> > The input of mdin.rep1 :
> > eplica Exchange MD
> > &cntrl
> > ntwx = 100, ntpr = 100,
> > ntt = 1, temp0 = 420.0, tempi = 0.0, tautp = 1.0,
> > igb = 2,
> > scnb = 2.0, scee = 1.2, dielc = 1, cut = 100.0,
> > ntb = 0, ntc = 2, ntf = 2,
> > nstlim = 5000, dt = 0.0020,
> > ntp = 0,
> > ibelly = 0, ntr = 0,
> > imin = 0, irest = 0, ntx = 1,
> > numexchg = 20, repcrd=1
> > /
> >
> > However, the error arise: mdfil : Error: unknown flag -ng
> >
> > in the amber 9 manual in page 166, the command is : $MPIRUN -np 16
> > sander -ng 8 -groupfile groupfile
> >
> > My command is similar to this.
> >
> > When I type sander -h
> > the informatin arise:
> > sander [-help] [-O] [-A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> > [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip rstdip -mdip
> > mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo -radii radii
> > ]
> >
> > I find there is no flag -groupfile,
> >
> > By the way, the sander imformation is some different for the amber 9
> > manual page 87:
> > sander [-help] [-O] [-A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> > -ref refc -x mdcrd -y inptraj -v mdvel -e mden -inf mdinfo -radii radii
> > -cpin cpin -cpout cpout -cprestrt cprestrt -evbin evbin
> >
> > Please give me any suggestion how to tackle this problem. Great thanks
> >
> >
> > Best wishes
>
>
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Received on Wed May 03 2006 - 06:07:05 PDT
