Re: [AMBER] problem on heating with restraints on the solute

From: Daniel Roe <>
Date: Sat, 20 Jul 2013 16:17:42 -0600


Are you talking about tutorial B1, step 5.1.5? Are you using the files
provided from the website (, polyAT_wat.prmtop,


On Sat, Jul 20, 2013 at 2:21 PM, John Travers <> wrote:
> Dear Amber experts
> I am a new user of AMBER. I am trying to run a MD simulation following the tutorial on simulating a DNA polyA-polyT Decamer. I got a problem at the heating stage. I used the SHAKE algorithm (the same as in the tutorial), but the MD only ran for 7 steps (stepsize 1fs) and stopped with the error message of segmentation fault. At the step 7, the kinetic energy term becomes NaN. On the other hand, if I don't use the SHAKE algorithm (ntc=1, ntf=1, time step=0.2 fs) the MD ran normally. Any hints on this?
> I also check the 6 step MD results using VMD, it seemed only a small part of the whole water was moving. I followed strictly the tutorial. The partial and full minimization went smoothly. I compared the structures before and after minimization, they looked just fine.
> Thanks!
> Best wishes
> JT
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sat Jul 20 2013 - 15:30:02 PDT
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