Dear Carlos Simmerling, you answered a previous question, saying that it is
possible to use ptraj to combine 2 mdcrd files from an original run and a
restarted run (your mail is at the end of this message). I can't find the way
to do it in the manual. Could you tell me how to do this please? Thank you.
Quoting Carlos Simmerling <carlos.csb.sunysb.edu>:
> you won't need the trajectory file to restart. later you can use ptraj
> to combine your mdcrd files from the original run and the restarted one.
> your input file is already set up for restarting so it looks OK.
> just make a new sander script where you change the input and output names.
> use the old restart file name as the new input coordinate file.
> I would use something like this (but you might do it differently):
> SANDER -O -i md2.in -o md2.out -p ph.parm -c eq_long.rst -r md2.rst -x
> md2.crd
>
> carlos
> ----- Original Message -----
> From: Do Anh Tuan
> To: amber.scripps.edu
> Sent: Wednesday, November 26, 2003 12:12 PM
> Subject: AMBER: restart MD program
>
>
> Dear amber users,
> I would like to run a MD simulation for few nanoseconds. But I don't know
> how to restart with the restrt (eq_long.rst) and mdcrd (eq_long.crd) files
> which are results of the previous MD simulation. Could somebody help me
> please? Thank you in advance.
>
> This is md.in file:
> -----------
> &cntrl
> imin=0,
> irest=1, ntx=7,
> iwrap=1,
> ntf=2, ntb=2,
> nstlim=1000000, dt=0.001,
> ntt=1, temp0=313.0, tautp=1.0,
> ntp=1, pres0=1.0, taup=1.2,
> ntc=2,
> ntpr=100, ntwx=2000, ntwr=1000,
> &end
>
> And sander command:
> ----------
> SANDER -O -i md.in -o eq_long.out -p ph.parm -c heat.rst -r eq_long.rst -x
> eq_long.crd
>
>
>
> D.A.Tuan
> Laboratory of Molecular Biotechnology
> University of Natural Sciences
> Vietnam National University - Ho Chi Minh City
> 227 Nguyen Van Cu St., Dist. 5, HCM City, Vietnam
>
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Received on Wed Jan 14 2004 - 15:53:01 PST
