I think I gave timings in the PNAS article on that, did you compare to them?
On 4/24/07, gurpreet singh <gps.iitm.gmail.com> wrote:
> Thanks Mr. Carlos for your reply
>
> i asked question on implicit simulation , that my implicit simulation of
> protein containing around 2500 atoms is going very slow as compared to
> explicit simulation of the same protein, u gave me the answer that large
> protein are usually slower to simulate in implicit , i am fully agree with u
> that because of the complex nature PB equation, for large protein this
> implicit simulations are usually slow
> but sir i have seen your papers on hiv-1 protease in which u have carried
> out 42 to 45 ns simulation using implicit solvent and that too without
> using any cut off, i think the reason for choosing the implicit was to carry
> more simulation in less time and to see those motions which is not possible
> to see in case of explicit solvent in less time span .
> sir i m also using the same enzyme hiv-1 protease which is having around
> 2500 atoms so why in my case this problem is coming.
>
> following are the files i m using in case of mini and equi
>
> imin=1,igb=2,cut=300.0,maxcyc=500,ncyc=250,ntr=1,ntb=0
> >
> >
> for equi
>
> imin=0,igb=2,cut=300.0,ntr=1,ntb=0,nstlim=20000,dt=0.002,ntc=2,ntf=2,
> tempi=10.0,temp0=300.0,ntt=1,tautp=2.0,ntp=0,ntpr=100,ntwx=0
>
>
>
> waiting for your reply
> thanks
>
>
>
>
>
>
>
>
>
>
> On 4/23/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> >
> > probably because you don't use a cutoff of 300 for explicit water
> simulation.
> > large proteins in implicit water are usually slower to simulate than
> > in explicit
> > water, there are more nonbonded pairs to calculate. explicit water usually
> > is done with periodic boundary conditions which can use methods like PME
> > to make the simulation faster..
> >
> > On 4/23/07, gurpreet singh <gps.iitm.gmail.com> wrote:
> > > Hello Amber users
> > >
> > > i m using Amber 9 to carry out implicit simulation of a protein
> molecule
> > > containing around 3000 atoms but i found that the mini. or equi. in
> implicit
> > > solvent is much slower than the mini or equi.in the explicit solvent ,
> i
> > > think for this much no of atoms the simulationshud be faster the
> explicit ,
> > > please tell me the reason for this unusual behaviour
> > >
> > > following are the input files i m using :
> > > for mini.
> > >
> > >
> imin=1,igb=2,cut=300.0,maxcyc=500,ncyc=250,ntr=1,ntb=0
> > >
> > > for equi.
> > >
> > > imin=0,igb=2,cut=300.0,ntr=1,ntb=0,nstlim=20000,dt=0.002,ntc=2,ntf=2,
> > > tempi= 10.0,temp0=300.0,ntt=1,tautp=2.0,ntp=0,ntpr=100,ntwx=0
> > >
> > >
> > > thanks
> > >
> > >
> > >
> >
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>
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Received on Wed Apr 25 2007 - 06:07:31 PDT
