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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Received on Wed Apr 25 2007 - 06:07:31 PDT
