AMBER Archive (2007)

Subject: AMBER: hybrid remd

From: Geoff Wood (geoffrey.wood_at_epfl.ch)
Date: Wed May 09 2007 - 06:22:09 CDT

>
Slightly from first email but essentially the same:
> To whom it may concern,
>
> I am attempting to run hybrid remd simulations with amber 9 but I
> find that I cannot get them started. I am probably making a simple
> mistake in the specification of the file names, any help would be
> much appreciated.
>
> The error I am getting is the following:
>
> ----------------------------------------------------------------------
> ----------
> 3. ATOMIC COORDINATES AND VELOCITIES
> ----------------------------------------------------------------------
> ----------
>
>
> FATAL: NATOM mismatch in coord and topology files
>
>
> This error appears in the stripped output file (i.e. a file called
> something like mdout.rep01.strip)
> In the full output file it looks as if the calculation has finished
> (the file is called mdout.rep01) i.e.
>
> Exiting runmd after getting initial energies for REMD 0
> wrapping first mol.: 1.009557807795775E-014 68.4142020000000
> 96.4591000000000
>
> ----------------------------------------------------------------------
> ----------
> 5. TIMINGS
> ----------------------------------------------------------------------
> ----------
>
> |>>>>>>>>PROFILE of Average TIMES>>>>>>>>>
>
>
>
>
>
> The groupfile looks like
>
> -O -i mdin.rep01 -o mdout.rep01 -p prm -c inpcrd.rep01 -r
> restrt.rep01 -x mdcrd.rep01 -inf mdinfo.rep01
> .
> .
> .
> .
>
> The input files look like:
>
> Full box (mdin.rep01)
>
> comment
> &cntrl
> imin = 0, irest = 1, ntx = 2,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 0.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> repcrd=0, numexchg=40, numwatkeep=350,
> nstlim = 1000, dt = 0.002,
> ntpr = 100, ntwx = 100, ntwr = 1000
> &end
> &ewald
> &end
>
> Reduced number of waters (mdin.rep01.strip)
>
> comment
> &cntrl
> imin = 0, irest = 1, ntx = 2,
> ntb = 0,
> igb=1,
> cut = 999, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 0.0, temp0 = 366.0,
> ntt = 3, gamma_ln = 1.0,
> repcrd=0, numexchg=40, numwatkeep=350,
> nstlim = 1000, dt = 0.002,
> ntpr = 100, ntwx = 100, ntwr = 1000
> /
>
>
> I have placed both the full parm file (prm) and reduced parm file
> (prm.strip) in the same directory. For the stripped parm I have
> tried with and without the counter ions that are present in the
> full calculation. I think it is preferable to omit them in a GB
> energy evaluation. The stripped parm was made using leap and a pdb
> that ptraj generated from a short md run involving the full system.
>
> The input coordinates are for the full system ( from a short md run
> for equilibration) and are placed in the same directory as
> inpcrd.rep01 etc.
>
> Thanks in advance,
>
> Dr Geoffrey Wood
> Ecole Polytechnique Fédérale de Lausanne
> SB - ISIC - LCBC
> BCH 4108
> CH - 1015 Lausanne
>
>
>
>

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