[gmx-users] GROMACS 4.5.4 keep crashing all the time

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Aug 18 04:03:30 CEST 2011

OK, here's my last few ideas:

1. Please try to repeat this with gen_vel set to the same value as  
your temperature coupling

2. Can you reproduce this in serial?

3. Can you reproduce this with the sd integrator?

4. Can you reproduce this with a simpler system? protein in vacuum or  
just water or remove the ions, etc?

5. Take the output .gro from 4.0.7 that ran fine for X ns and run it  
under 4.5.4. Do you get the same lincs warnings?

6. Also, note that you are getting warnings and the run does not  
actually crash but just stops after too many warnings. So what are  
atoms 981 and 982? Does their motion look different in an important  
ways between the 4.0.7 and 4.5.4 trajectories?


-- original message --

Hi Chris,

thanks for the advice, I have to say I tried this as well without any success.


On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote:

> run an EM with flexible water. I often find that this is the only  
> way to get a stable system. 500 steps of steep with  
> define=-DFLEXIBLE (or different depending on your water model I  
> think) should be enough.
> Chris.
> Hi Chris and Justin,
> On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:

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