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
>
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Received on Fri Jul 09 2010 - 04:00:03 PDT
