AMBER Archive (2007)

Subject: Re: AMBER: Fwd: a request

From: santanu roy (66.santanu_at_gmail.com)
Date: Sat Jan 27 2007 - 00:34:15 CST

ok, just correct me if I have understood you properly, after minimization
iof the whole system is done I will take the system to a temperature say
300 k at constant volume condition using MM only for say 30 ps, then I
will remove the constant volume condition and allow the system to relux and
constant pressure condition to switch on, and this constant temperature &
pressure condition along with the relaxation of the system will be
carried out bye qmmm method for say 300 ps

I hope this is what you meant.
Santanu

On 1/25/07, Gustavo Seabra <gustavo.seabra_at_gmail.com> wrote:
>
> You are welcome.
>
> But before you do that, I just wanted to clarify one point: before you
> use qm/mm for production, you do need to relax the system for a while,
> using qm/mm. You will find that, even if you equilibrate the system
> using MM first, when you change to qm/mm the system will most likely
> *not* be in equlibrium, and you'll need to relax it (with qm/mm)
> *before* doing any qm/mm production run.
>
> Good luck,
>
> Gustavo.
>
> On 1/25/07, santanu roy <66.santanu_at_gmail.com> wrote:
> > Dear Sir,
> > Thank you very much for your reply. Before getting your
> reply I
> > solved the problem, actually
> > it was the large no. of atoms within the qm part , which made the
> problem,
> > saying infinite formate loop,
> > When I discarded some atoms, I got the result.
> >
> > But I will follow the way you have showed me, I will use qmmm method
> during
> > productive run only.
> > That could be the best thing.
> > Thanks again
> > Santanu
> >
> > On 1/25/07, Gustavo Seabra <gustavo.seabra_at_gmail.com> wrote:
> > >
> > > Hi,
> > >
> > > As for the atom numbers, your scheme seems OK. The numbers you get
> > > from the PDB file should be correct. You can also try the 'writepdb'
> > > optioin in the qm/mm namelist, that will give you a pdb file with just
> > > the QM region, so you can check your system.
> > >
> > > Note that you can also use 'QMMASK' to set the QM region. That may be
> > > easier than listing atom-by-atom.
> > >
> > > Now, there's one thing I would *not* recommend you to do, and it is
> > > running the first minimization (just to remove bad contacts) already
> > > with QM. At leas in my experience, you may run into lots of
> > > convergence problems there. You should first minize the system using
> > > just MM, then try to take it to the desired temperature first, all
> > > using MM. AFTER that, you can change part of the system to QM, and
> > > then relax the system for a while more. This procedure seems to work
> > > best for me. (Ross, comments?)
> > >
> > > Gustavo.
> > > P.S. If you are running into problems with putting all files in gmail,
> > > you can try to tar all files together and send just one tar file.
> > >
> > > On 1/25/07, santanu roy < 66.santanu_at_gmail.com> wrote:
> > > >
> > > > Sir, I could not send prmtop and inpcrd file, gmail problem.
> > > > looking forward for your reply.
> > > >
> > > >
> > > > ---------- Forwarded message ----------
> > > > From: santanu roy < 66.santanu_at_gmail.com>
> > > > Date: Jan 25, 2007 12:42 PM
> > > > Subject: Re: a request
> > > > To: Ross Walker <ross_at_rosswalker.co.uk >
> > > >
> > > >
> > > >
> > > > Dear Sir,
> > > > Let me tell you what I am actually doing. I am
> using
> > AMBER
> > > > qmmm method for simulating Thermolysin. Some part of the Active site
> > > > has been kept into the QM region and other part obviously moves into
> the
> > > > MM region. I , atfirst, using Xleap solvated the system of
> interest
> > i.e.
> > > > thermolysin using solvatebox command. Then I made
> thermolysin.prmtop
> > > > and thermolysin.inpcrd file. Then using ambpdb command I made
> > > > solvated_thermolysin.pdb , i.e. using parameter and coordinate file
> and
> > > > ambpdb command I have got a new pdb file of solvated thermolysin.
> > > >
> > > > Now, I have to minimise the solvated thermolysin, so atfirst my job
> > would
> > > > be to minimise the water solvant keeping thermolysin fixed. There I
> > found
> > > > the problem. in iqmatoms=......, I took the atom no. from the
> newly
> > > > formed solvated_thermolysin.pdb. I have a doubt over here, as when
> we
> > > > run the command for minimisation only prmtop and inpcrd file
> information
> > > > are given, so if we use atom no. in qmmm key , taken from
> > > > Solvated_thermolysin.pdb which is made from prmtop and inpcrd file,
> > > > will that be correct? Actually there is no other way to assign atom
> no.
> > in
> > > > qmmm key I have found. I think I am right in this case.
> > > >
> > > > I am attaching the input and output file, and also prmtop & inpcrd
> > file,
> > > > solvated_thermolysin.pdb file.
> > > >
> > > > I am using SGI ALTIX, MPIRUN, sometimes using 8 parallel processor
> > > > and sometimes 4 parallel processor.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On 1/24/07, Ross Walker < ross_at_rosswalker.co.uk > wrote:
> > > > >
> > > > >
> > > > > Hi Santanu,
> > > > >
> > > > > The input format for QMMM with link atoms is identical to QMMM
> without
> > > > link atoms. Sander takes care of all the link atom treatment for you
> > > > automatically. The best is if you can send me the calculation you
> are
> > > > running so I can take a look at it. Please send me the mdin, prmtop
> and
> > > > inpcrd files as well as the output file where you are having
> problems.
> > > > >
> > > > > It would also be useful to know what system (OS, processor etc)
> you
> > are
> > > > running this on, what compilers you used. Is this serial or
> parallel?
> > And
> > > > which bugfixes have been applied to the Amber installation?
> > > > >
> > > > > All the best
> > > > > Ross
> > > > >
> > > > > /\
> > > > > \/
> > > > > |\oss Walker
> > > > >
> > > > > | HPC Consultant and Staff Scientist |
> > > > > | San Diego Supercomputer Center |
> > > > > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > > > > | http://www.rosswalker.co.uk | PGP Key available on request |
> > > > >
> > > > > Note: Electronic Mail is not secure, has no guarantee of delivery,
> may
> > not
> > > > be read every day, and should not be used for urgent or sensitive
> > issues.
> > > > >
> > > > >
> > > > >
> > > > > ________________________________
> > > > From: santanu roy [mailto:66.santanu_at_gmail.com]
> > > > > Sent: Wednesday, January 24, 2007 01:11
> > > > > To: Ross Walker
> > > > > Subject: Re: a request
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Dear Sir,
> > > > > Thank yoy very much for your reply. I have got my
> > answer.
> > > > > But I am facing problem while silmulating qmmm system.
> > > > >
> > > > > Can you please send me the input formate for qmmm with link atom
> > method.
> > > > Neither in the tutorial , nor in the manual the qmmm formate
> including
> > link
> > > > atom is given. I myself tried out, but getting some error like
> > > > > 'aborting' .
> > > > >
> > > > > I will be highly obliged if you kindly respond.
> > > > > Thanking you,
> > > > > Santanu
> > > > >
> > > > >
> > > > >
> > > > > On 1/17/07, Ross Walker <ross_at_rosswalker.co.uk > wrote:
> > > > > >
> > > > > >
> > > > > > Dear Santanu,
> > > > > >
> > > > > > I'm not entirely sure I understand your question correctly.
> However,
> > I
> > > > assume you are refering to the first amber tutorial on modelling
> DNA.
> > Here
> > > > we start doing gas phase simulations where we run two simulations,
> one
> > > > without a cutoff and one with. The key point here is that the cutoff
> > > > simulation gives a stable system but the no-cutoff simulation does
> not.
> > Thus
> > > > one could make the "wrong" conclusion that the cutoff sim is giving
> the
> > > > correct result. However, these simulations are in a vacuum at 300K.
> If I
> > > > really took a 10mer of DNA and heated it up to 300K in a vacuum it
> would
> > not
> > > > be stable - the two chains would alsmost certainly come apart and
> the
> > > > molecule would decompose. Thus the no-cutoff simulation is probably
> > correct.
> > > > > >
> > > > > > The important point is that using a cutoff is 'never' a good
> idea.
> > You
> > > > can get away with something liek 16 angstroms or more in an implicit
> > solvent
> > > > GB simulation as there is a dielectric screening factor that reduces
> > things
> > > > by a factor of 80. However, realisticlly here one should not use a
> > cutoff if
> > > > one can afford it computationally. Electrostatic interactions are so
> > long
> > > > ranged that you have to go to 30 or 40 angstroms before you get down
> to
> > > > noise.
> > > > > >
> > > > > > However, with PME doing periodic boundaries the situation is
> > slightly
> > > > different. You should probably read up on thePME method from the
> papers
> > > > cited in the Amber manual and make sure you understand the
> mathematics.
> > > > Essentially what you do is take what is a divergent (infinite) sum
> of
> > pair
> > > > wise interactions in real space and cast it into a convergent sum in
> > > > reciprocal space. You then use an FFT to calculate the reciprocal
> space
> > > > contribution. You still have a cutoff of say 8 angstroms or so to
> > account
> > > > for VDW interactions and also for load balancing issues. This way 8
> > > > angstroms worth of electrostatics is done in the direct space sum
> within
> > the
> > > > cutoff while the remainder is done in reciprocal space and adjusted
> by
> > an
> > > > erfc function (error function) to go to zero at the cutoff. In this
> way
> > PME
> > > > gives you effectively infinite electrostatics without requiring you
> to
> > > > calculate infinite pairwise interactions. Hence why you can
> essentially
> > use
> > > > a cutoff with periodic boundaries without problems - as LONG AS YOU
> ARE
> > > > USING PME.
> > > > > >
> > > > > > I hope this helps explain things. Note if you further questions
> it
> > is
> > > > probably best to post them to the Amber mail reflector - see
> > > > http://amber.scripps.edu for details on how to subscribe.
> > > > > >
> > > > > > All the best
> > > > > > Ross
> > > > > >
> > > > > > /\
> > > > > > \/
> > > > > > |\oss Walker
> > > > > >
> > > > > > | HPC Consultant and Staff Scientist |
> > > > > > | San Diego Supercomputer Center |
> > > > > > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > > > > > | http://www.rosswalker.co.uk | PGP Key available on request |
> > > > > >
> > > > > > Note: Electronic Mail is not secure, has no guarantee of
> delivery,
> > may
> > > > not be read every day, and should not be used for urgent or
> sensitive
> > > > issues.
> > > > > >
> > > > > >
> > > > > >
> > > > > > ________________________________
> > > > From: santanu roy [mailto: 66.santanu_at_gmail.com]
> > > > > > Sent: Friday, January 12, 2007 08:31
> > > > > > To: amber_tutorial_query_at_rosswalker.co.uk ;
> > > > ross_at_rosswalker.co.uk
> > > > > > Subject: a request
> > > > > >
> > > > > >
> > > > > >
> > > > > > Dear Sir,
> > > > > > I have gone through almost all of the amber
> > tutorial,
> > > > and tested it.
> > > > > >
> > > > > > I have some basic questions as the following
> > > > > > 1) why we generally take cutoff as 8 to 10 angstrom? in this
> case
> > we
> > > > get actually correct result, why? in case of no cutoff we get
> > > > > > worst result. why?
> > > > > > is it like VDW interaction, electrostatic interaction get very
> less
> > > > value, so we should ignore those interaction after that cut off?
> > > > > > and in case of no cut off we consider those interactions, is
> it the
> > > > reason for unstable result?
> > > > > >
> > > > > > 2) does cut off affect on periodic boundary condition?
> > > > > >
> > > > > > I am looking forward for your answer.
> > > > > > Regards
> > > > > > Santanu Roy
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