Hi Gustavo,
Thank you for your comment. It is a very important issue.
I have not run any simulation with amber, but just through an example from
the mailing list.
I would be very grateful if you can give me further suggestion and comment.
Yes my system contains 10 ~ 15k atom, ~5k for not quite flexible carbon
nanotubes, others for flexible molecules.
Gromacs indicates that I need 6 years to run 1ns simulation without parallel
run.
A post by a user in amber said he/she simulate 15k atom with implicit
solvent, and it will be ~60 days for 1 ns without parallel run.
I assume that:
1: I can use amber with implicit solvent and use parallel run.
2: ~5k CNT carbons are relatively rigid and may not require much computation
time for surface geometry calculation in implicit solvent case.
3. The parallel I can access gives ~15X for either amber or gromacs.
Any input is welcome!
Yan
On Fri, Jul 9, 2010 at 3:50 AM, Gustavo Seabra <gustavo.seabra.gmail.com>wrote:
> Are you sure you *need* implicit solvent for this calculation?
>
> For large systems, implicit solvent calculations can get slow,
> sometimes even slower than explicit solvent ones.
>
> Gustavo.
>
>
>
> On Fri, Jul 9, 2010 at 1:51 AM, Yan Gao <yan.gao.2001.gmail.com> wrote:
> > Thanks Jason.
> >
> > Yes I also feel that would be tricky. But The carbon nanotube has quite
> > tricky structure that if you break a tube into two for topology purpose
> > (with antechamber), when putting their topology together, I feel that I
> need
> > to manually add a lot of bond/angles/dihydrals. And I may need to use
> > different sized nanotubes.
> >
> > As for why I changed from gromacs to amber. I want to simulate ~ 15k
> atoms
> > containing nanotubes and polymers. It may take gromacs >100 years for 1
> ns
> > with explicit water.
> > And I was told that amber has the best implicit solvent simulation
> ability.
> >
> > BTW. It seems that gromacs has coarse-grain ability but no implicit
> solvent,
> > while amber has implicit solvent but no coarse-grain.
> >
> > Yan
> >
> > On Thu, Jul 8, 2010 at 8:26 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> >
> >> On Thu, Jul 8, 2010 at 7:26 PM, Yan Gao <yan.gao.2001.gmail.com> wrote:
> >>
> >> > Thanks Bill.
> >> >
> >> > I am going to take your advice and try to write a program to convert
> the
> >> > gromacs topology to amber's.
> >> >
> >>
> >> This could be quite tricky. In order to do this, you'll have to
> understand
> >> both types of topology files as well as how to convert one into the
> other.
> >> Understanding the Amber topology file itself is very difficult. You'd
> >> probably be better off using pre-established programs to create your
> >> topology file(s).
> >>
> >> I have another question regarding the force field.
> >> > I use customized FF in gromacs, so I would wish to keep it customized
> in
> >> > amber. May I know if it is doable? And if a customized FF will
> physically
> >> > conflicted with the implicit solvent which I want to apply? (Or if the
> >> > result be un-trustable ) Thanks.
> >> >
> >>
> >> Why are you trying to switch to Amber? Is there something you can do
> with
> >> Amber that you can't with gromacs?
> >>
> >>
> >> Good luck!
> >> Jason
> >>
> >>
> >> > I am also will include free ions in the system with implicit solvent.
> >> Will
> >> > the free ions be an issue? Thanks.
> >> >
> >> > Regards,
> >> > Yan
> >> >
> >> > On Thu, Jul 8, 2010 at 2:28 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >> >
> >> > > > I want to simulate carbon nanotubes (CNT) with implicit water, so
> I
> >> > need
> >> > > to
> >> > > > translate the topology from Gromacs format to Amber format.
> >> > >
> >> > > > I tried antechamber using the pdb file, planning to manually
> modify
> >> the
> >> > > > parameters after the file is constructed. However my tube is big
> >> (1200
> >> > > > carbon atoms), and antechamber said "The atom number exceeds the
> >> > MAXATOM,
> >> > > > reallocate memory", and eventually crashed.
> >> > >
> >> > > > I also think of divide the long tube into small ones, but it seems
> >> that
> >> > I
> >> > > > need to manually add the bond/angle/dihydral to connect the small
> >> > tubes.
> >> > > The
> >> > > > number of connections seems to be quite large, and I am not quite
> >> know
> >> > of
> >> > > > how to add it. So I still look for a better way of doing it.
> >> > >
> >> > > You will need bond, angle and dihedral parameters whether the
> >> > > molecule is one residue or many. But specifying the many
> >> > > connections between multiple smaller residues could be a chore.
> >> > > You might want to write a program to generate the leap cmds
> >> > > to do this. It might also be tricky to turn a 1-residue pdb
> >> > > into a multi-residue pdb; if the 1-res pdb was generated by
> >> > > a program, you may want to modify that program.
> >> > >
> >> > > Given all that, it may be worth trying to debug antechamber
> >> > > to allow the 1-res version.
> >> > >
> >> > > Bill
> >> > >
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >
> >> >
> >> >
> >> >
> >> > --
> >> > Yan Gao
> >> > Jacobs School of Engineering
> >> > University of California, San Diego
> >> > Tel: 858-952-2308
> >> > Email: Yan.Gao.2001.gmail.com
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Graduate Student
> >> 352-392-4032
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Yan Gao
> > Jacobs School of Engineering
> > University of California, San Diego
> > Tel: 858-952-2308
> > Email: Yan.Gao.2001.gmail.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: Yan.Gao.2001.gmail.com
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Received on Fri Jul 09 2010 - 07:00:03 PDT
