AMBER Archive (2007)

Subject: Re: AMBER: hybrid remd

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu May 10 2007 - 06:20:14 CDT

have you checked the number of atoms in your strip prmtop and
compared to the # of atoms sander is producing in the .strip restart
files?

On 5/9/07, Geoff Wood <geoffrey.wood_at_epfl.ch> wrote:
>
> Hi Carlos,
> Thanks for clearing up that issue for me. I just wanted to return to the
> original problem I was having. For my system, I have a full periodic set
> of files and a set of files for the stripped non-periodic system. I also
> have a coordinate file for the stripped system, since I created the parm and
> the corresponding crd files in leap.
>
> If I forget about running the hybrid calculation and run a standard remd
> simulation on the full system then it runs without problems.
> Alternatively, if I run a standard remd run on the reduced system then it
> also runs without problems. This suggests that there is no problems with my
> crd or parm files in both cases.
>
> However, when I attempt to run the hybrid calculation then I get the error
> that I reported. From our correspondence would you be able to shed light on
> why this may be happening?
>
> Cheers,
>
> Dr Geoffrey Wood
> Ecole Polytechnique Fédérale de Lausanne
> SB - ISIC - LCBC
> BCH 4108
> CH - 1015 Lausanne
>
>
>
>
> On May 9, 2007, at 11:18 PM, Carlos Simmerling wrote:
>
> 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_at_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_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.rep01etc.
> > >
> > > 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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