Hi,
You can use the setvelocity command in cpptraj to assign velocities from a
Maxwell Boltzmann distribution at a target temperature before writing to
restart. These can be corrected for shake constraints as well. See the
manual for full details.
On Thu, Sep 3, 2020 at 10:45 PM Lod King <lodking407.gmail.com> wrote:
> Hi, Bill
>
>
>
> That is correct. so I changed the input file with the following flags,
>
> irest=0
>
> ntx=1,
>
> restart a new simulation and do not read the velocity, but because I ran
>
> aMD, I end up having a new problem:
>
>
>
> cudaMemcpy GpuBuffer::Download failed an illegal memory access was
>
> encountered
>
>
>
> What is your suggestion if I need to continue a new MD with a frame
>
> extracting from the middle of an old aMD?
>
>
>
>
>
> On Thu, Sep 3, 2020 at 7:19 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>
>
> > When you convert to pdb, you lose the velocities.
>
> >
>
> > Bill
>
> >
>
> > On 9/3/20 6:03 PM, Lod King wrote:
>
> > > Hello AMBER
>
> > >
>
> > > I extracted one frame and saved as pdb file, then I converted it to
> rst7
>
> > > file such that I can restart a new MD using that restart file,
> however, I
>
> > > encountered the following error in the output file:
>
> > >
>
> > > $ cpptraj -p protein_water.prmtop -y 1346.pdb -x 1346.rst7
>
> > >
>
> > > | ERROR: I could not find enough velocities in 1346.rst7
>
> > >
>
> > > Can someone specify ?
>
> > > _______________________________________________
>
> > > AMBER mailing list
>
> > > AMBER.ambermd.org
>
> > > http://lists.ambermd.org/mailman/listinfo/amber
>
> > --
>
> > Phobrain.com
>
> >
>
> > _______________________________________________
>
> > AMBER mailing list
>
> > AMBER.ambermd.org
>
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> >
>
> _______________________________________________
>
> AMBER mailing list
>
> AMBER.ambermd.org
>
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 04 2020 - 10:30:02 PDT
