I think that extracting it using ptraj is much safer.
However, 1ns is pretty short so I think the best thing is
to rerun it and solve the problem. You want to find out
what's wrogn anyway.
Amit Kumar wrote:
> 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
> <mailto: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>
> > <mailto: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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> >
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Received on Sun Jan 21 2007 - 06:07:24 PST
