# Re: AMBER: Fwd: a request

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Thu, 25 Jan 2007 10:49:49 -0500

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.gmail.com> wrote:
> Dear Sir,
> 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.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.gmail.com> wrote:
> > >
> > > Sir, I could not send prmtop and inpcrd file, gmail problem.
> > >
> > >
> > > ---------- Forwarded message ----------
> > > From: santanu roy < 66.santanu.gmail.com>
> > > Date: Jan 25, 2007 12:42 PM
> > > Subject: Re: a request
> > > To: Ross Walker <ross.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.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.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.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
> > > > 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
> > > 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.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.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.gmail.com]
> > > > > Sent: Friday, January 12, 2007 08:31
> > > > > To: amber_tutorial_query.rosswalker.co.uk ;
> > > ross.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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Received on Sun Jan 28 2007 - 06:07:21 PST
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