Re: AMBER: hybrid remd

From: Asim Okur <asimokur.gmail.com>
Date: Wed, 9 May 2007 15:07:59 -0400

Hi,

Before running Hybrid Solvent REMD you should read the manual and the
article (Okur, Roe, Cui, Hornak and Simmerling, JCTC, 2007) especially
the warnings in the manual (Page 168).

Your hybrid topology file should have exactly the same number of
waters as the reduced system generated by sander. Use of counterions
has not been implemented/tested with hybrid remd and should not be
used.

Also, I see in your GB calculations (mdin.rep01.strip) you set nstlim
= 1000. You should not do any dynamics during the GB step. Just single
step energy evaluation is needed. You can see examples of input files
in the remd and hybrid remd test cases in amber9.

I hope this helps,

Asim

-- 
Asim Okur, Ph.D.
Stony Brook University
Chemistry Department
Stony Brook, NY 11733
(631) 632 1560
On 5/9/07, Geoff Wood <geoffrey.wood.epfl.ch> wrote:
>
>
>
> 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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Received on Sun May 13 2007 - 06:07:13 PDT