Dear Amber Users,
I was trying to apply GaMD to a membrane protein system with Amber20. I did 100 ns regular MD equilibration and the last 10 ns was used to calculate the parameters for GaMD. Then 50 ns GaMD equilibration. Some parameters in the input file for this stage are:
ntx=1, irest=0, nstlim=75000000,
igamd = 3, iE = 1, irest_gamd = 0, ntcmd = 50000000, nteb = 25000000, ntave = 500000, ntcmdprep = 45000000, ntebprep = 1500000, sigma0P = 6.0, sigma0D = 6.0,
This stage was complete successfully. Then I performed the production run with the following key parameters:
ntx=1, irest=0, nstlim=25000000,
igamd = 3, iE = 1, irest_gamd = 1, ntcmd = 0, nteb = 0, ntave = 500000, ntcmdprep = 0, ntebprep = 0, sigma0P = 6.0, sigma0D = 6.0
However, I immediately encountered this error and could not restart the simulation: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
When I changed ntx to 5 and irest to 1, there was no such problem for the production run. Can I ask why the reinitialization of velocity could not be done in this case? Thank you!
Best,
Haoxi
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Received on Fri Jan 21 2022 - 09:00:02 PST
