[AMBER] Query regarding Dialanine peptide 2d ABMD tutorial in the NFE category

From: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Date: Wed, 30 Sep 2020 09:41:02 +0000

Respected AMBER community,
              I was following the ABMD dialanine peptide tutorial for generating the 2D Free energy profile using multiple walker method. I was able to successfully complete the first step, however, in the second step of the tutorial where 4 walkers are used, I encountered the following error :
 Running multipmemd version of pmemd Amber18
    Total processors = 40
    Number of groups = 4

vlimit exceeded for step ******; vmax = 26.2469
vlimit exceeded for step ******; vmax = 26.0264

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
I looked in the amber docs if there was some way to set vmax, but I did not find anything.

I have tried this simulation twice, and it has given me the same error at both times.
All I have changed from the tutorial is the number of processors I have used in MPI, and the normal version of pmemd.MPI instead of pmemd.cuda.MPI :

mpirun -np 40 pmemd.MPI -O -ng 4 -groupfile groups

Instead of
mpirun -np 4 pmemd.cuda.MPI -O -ng 4 -groupfile groups

I am currently running Amber18, instead of Amber16 software used in the tutorial.
Could anyone guide me on how to fix this error, or what could be the potential source of it? Any help would be highly appreciated.

Madhur Aggarwal,
4th Year Undergraduate at IIIT Hyderabad
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Received on Wed Sep 30 2020 - 03:00:02 PDT
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