AMBER Archive (2006)

Subject: Re: AMBER: about the execuation of REMD with sander of amber9

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Sat Apr 29 2006 - 08:43:46 CDT

amber8 remd does not use group files. amber9 does.
here is an example of an amber8 remd sander input:

sander -O -ng 16 -rem 1 -remlog remlog \
-i rem.in -p prmtop -c inpcrd -o rem.out \
-x rem.x -e mden -v mdvel -inf reminfo -r rem.r

sander appends .000, .001 etc to the input and output
files.

pang zhao wrote:

> Dear All,
>
> I use sander module of amber8 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
> If perform remd with amber8, how to execute it?
>
> Best wishes

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