AMBER Archive (2007)

Subject: Re: AMBER: Fwd: a request

From: santanu roy (66.santanu_at_gmail.com)
Date: Thu Jan 25 2007 - 07:15:08 CST

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
> > > >
> > > >
> > >
> > >
> >
> >
> >
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu