Hi Carolos,
I was planning to extract the 1000ps frame using the VMD. Then use leap to
convert the pdb to crd.
I read in one of the message in the amber archieve that one will lose the
velocity information. My understanding is that it is very vital to have the
velocity information, especially when you are restarting the MD. Whats your
comment??
Amit
On 1/18/07, Carlos Simmerling <carlos.csb.sunysb.edu> wrote:
>
> do you mean from the trajectory file? Where is the pdb coming from?
> You can use ptraj to extract a frame of the traj file to a restart format
> and use that, but you lose some precision (and no velocities).
>
>
> Amit Kumar wrote:
>
> > Thanx ....
> >
> > I also wanted to know if it is fine to generate a crd file from the
> > pdb file using tleap and then restarting the simulation. Will I be
> > losing some information.
> >
> > Amit
> >
> > On 1/18/07, *Carlos Simmerling* <carlos.csb.sunysb.edu
> > <mailto:carlos.csb.sunysb.edu>> wrote:
> >
> > I'm not sure, it could be file system problems or
> > other things, but you might want to try writing the
> > restart more often (ntwr of 500 or so).
> > Try re-running and see if it is reproducible or not.
> >
> >
> > Amit Kumar wrote:
> >
> > > Hello Amber users,
> > >
> > > I am doing simulations is parallel using sander.MPI command in
> > Amber9.
> > > I did 1 ns simulation. The output file (md.out) shows that the 1
> ns
> > > simulation was completed
> > > successfully. But when I opened the restrt file and it shows the
> > > co-ordinate for 860 ps instead of 1000 ps. And when I restart the
> > > simulation it starts at 860 ps instead of 1ns, but the mdout file
> > > shows the simulation went on well till 1ns. I am not sure why my
> > > restrt file doesn`t have final crd for 1000ps. My input file for
> the
> > > MD simulation was
> > >
> > > MD Generalise Born, no cut off
> > > &cntrl
> > > imin = 0, ntb = 0,
> > > igb = 5, ntpr = 100, ntwx = 1000,
> > > ntt = 3, gamma_ln = 1.0,
> > > tempi = 300.0, temp0 = 300.0,
> > > nstlim = 500000, dt = 0.002,
> > > cut = 999, ntwr = 10000,
> > > /
> > >
> > > I will appreciate your comments.
> > >
> > > Amit
> >
> >
> >
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Received on Sun Jan 21 2007 - 06:07:24 PST
