Aaron Fafarman wrote:
Dear GMX-community,
I'm running four related, equilibrium-dynamics simulations of a small
protein in explicit water, each with a different non-natural
amino-acid in the sequence. One of the four non-natural amino-acid
containing proteins can be simulated for long times, up to 4 ns
without incident, but the other three invariably crash. On repeated
reinitialization (changing the box size, changing the duration of
position restrained refinement) they still keep crashing at any time
between 100's of picoseconds and 2 ns. Usually an error such as
"3009.270 ps: Water molecule starting at atom 26883 can not be
settled." is printed to the log file and the pdb of the step after the
crash has nonsense numbers for the coordinates of the offending water
molecule. It's always a different water molecule, always a
high-numbered atom (>20000). The crashes happen on both a
self-compiled linux build and on a self-compiled Mac OS 10.4 build,
both GMX 3.3.1. A simulation of just the parameterized amino acids in
a box of water never crashes over the course of a 4 ns simulation so I
don't suspect my amino-acid parameters.
As a general reference, check out the following:
http://wiki.gromacs.org/index.php/blowing_up
For debugging purposes, I have found that if I set nstxout = 1 in the .mdp file,
I can usually capture the initial events leading to the explosion.
Unfortunately, the water molecule that cannot be settled is usually an
unfortunate victim of another molecule that has gone flying off across your system.
It might also be useful to post your .mdp file here if you are still unable to
find the problem.
-Justin
I'm using ffamber99 and I parameterized the amino acids myself using
antechamber and amb2gmx. I'm using ffamber_tip3p. Thanks for reading.
-Aaron
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
