Hi,
You may want to try the system preparation protocol outlined here:
https://aip.scitation.org/doi/abs/10.1063/5.0013849
This has been implemented in a script for Amber here:
https://github.com/drroe/AmberMdPrep
Hope this helps,
-Dan
On Thu, Mar 24, 2022 at 1:05 AM Anita Meena
<Anita.Meena.cys20.chemistry.iitd.ac.in> wrote:
>
> Dear Amber users,
>
> I am trying to simulate a protein in water. I have successfully
> generated the topology (.top) and coordinate (.rst) files using tleap.
> I am getting the following error while minimization, particularly in the
> minimization of water.
>
> cudaMemcpy GpuBuffer::Download failed an illegal memory access was
> encountered.
> And this didn't give results in the output file (min_wat.out) and didn't
> generate the coordinate file.
>
> I used the following command for minimization:
>
> pmemd.cuda -O -i min_wat.in -o min_wat.out -p job_solv.top -c
> job_solv.rst -r min_wat.rst -ref job_solv.rst.
> ----------------------------------------------------------------------------------------------------
> Here is the min_wat.in, I used
>
> Minimize water
> System minimization:
> &cntrl
> imin=1, ntmin=1, nmropt=0, drms=0.1,
> maxcyc=10000, ncyc=7000,
> ntx=1, irest=0,
> ntpr=500, ntwr=500, iwrap=0,
> ntf=1, ntb=1, cut=5.0, nsnb=5,
> igb=0,
> ibelly=0, ntr=1,
> restraintmask="!:WAT", restraint_wt=10.0,
> &end
> /
> ----------------------------------------------------------------------------------------------------
> I also tried the same for 3 steps using pmemd.cuda (setting ntpr=ntwr=1)
> but the same problem popped up.
>
> When I did it using the sander.MPI and it worked.
>
> Can someone explain, why it's showing problems with pmemd.cuda.
>
> Thanks and regards,
>
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Received on Thu Mar 24 2022 - 10:00:02 PDT
