Re: [AMBER] Segmentation Fault with pmemd

From: David A Case <>
Date: Sat, 29 Aug 2015 07:42:34 -0400

On Sat, Aug 29, 2015, Ziheng Wang wrote:
> I am simulating a small protein system with a Mg2+ GTP bound (Mg2+
> params from frcmod.) I am using frcmod.ionslm_1264_tip3p for metal
> parameters and for
> GTP parameters. I was able to generate prmtop and inpcrd for the
> system. However, I get this error message when running pmemd.cuda:

> Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
> The system is able to minimize fine with pmemd. The same error occurs
> during MD when I run pmemd without cuda.

Usual debugging advice: set nstlim to some small value (say 100), and ntpr and
ntwx to 1. See what happens (use the CPU version in serial). Is the energy
at the start of MD the same as at the end of minimization? Does it fail on
the first step or later? If later, look at the structures in the mdcrd file
to see if you can find problems.


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Received on Sat Aug 29 2015 - 05:00:06 PDT
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