AMBER Archive (2007)

Subject: Re: AMBER: hybrid remd

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed May 09 2007 - 15:52:03 CDT

Hi Geoff, yes that's true, I think that it's not so much that sander will
get confused as it might
cause problems in the centering/imaging and possible inability to get a
single set of
coordinates with a complete solvent shell around multiple solutes. This
isn't a problem in the
fully solvated system during MD due to the periodicity, but the hybrid
calculation
is done without periodicity. As far as ions go, I think one needs to have
the same
caution as with explicit counterions and any implicit solvent- we're not
sure how well
they work or what the limitations are, so treat it cautiously and only try
it after you're
sure you understand what you are doing without them.
carlos

On 5/9/07, Geoff Wood <geoffrey.wood_at_epfl.ch> wrote:
>
> Hello Asim,
>
> Thank you very much for your suggestions they were very helpful. I have
> made sure that the topology and number of waters correspond to what sander
> is expecting. That being said, I haven't been able to make much progress.
> If I understand your email correctly then any attempt to run hybrid remd
> with counter-ions will cause sander to get confused as to what is solute and
> solvent? If this is the case, then would the same be true if I decided to
> run a hybrid remd run with more than one solute (say a dimer of two
> proteins)?
>
> Thanks in advance,
>
> Dr Geoffrey Wood
> Ecole Polytechnique Fédérale de Lausanne
> SB - ISIC - LCBC
> BCH 4108
> CH - 1015 Lausanne
>
>
>
>
> On May 9, 2007, at 9:07 PM, Asim Okur wrote:
>
> 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_at_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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