exactly. you need to be careful because they may not actually have full
solvent shells.
also you need to make sure you keep enough water to solvate both solutes.
On 5/9/07, Geoff Wood <geoffrey.wood.epfl.ch> wrote:
>
> Hi Carlos,
> Thankyou for your response to my questions. I am still slightly confused
> (its just not only sander) so I just wanted to clarify what you have said.
> Sander should be able to run the simulation with multiple solutes but it is
> unclear how meaningful the results will be?
>
> Dr Geoffrey Wood
> Ecole Polytechnique Fédérale de Lausanne
> SB - ISIC - LCBC
> BCH 4108
> CH - 1015 Lausanne
>
>
>
>
> On May 9, 2007, at 10:52 PM, Carlos Simmerling wrote:
>
> 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.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.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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> >
> >
> >
>
>
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Received on Sun May 13 2007 - 06:07:15 PDT
