> What is your suggestion if I need to continue a new MD with a frame
extracting from the middle of an old aMD?
Equilibrate to give it valid velocities, just as you would a new model.
Bill
On 9/3/20 7:45 PM, Lod King 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
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Received on Thu Sep 03 2020 - 23:00:03 PDT
