AMBER Archive (2007)

Subject: AMBER: hybrid remd

From: Geoff Wood (geoffrey.wood_at_epfl.ch)
Date: Wed May 09 2007 - 05:15:16 CDT

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 = 0, ntx = 1,
   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 = 0, ntx = 1,
   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 (I have tried both from
a minimization and 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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