[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broke

[Chih-Ying Lin]

Hi
>From Tsjerk,
"Previously you had an issue with the addition of ions to your .top
file. In your protocol, it's not mentioned. Have you made sure that
issue is cleared?"   => Yes, I did.



I encountered two cases that my simulation broke.
Case I => 6LYZ + ligands + water molecules + CL-
           => Gromacs 3.3.3
           => error from the addition of ions to my .top file
           => The problem is solved and the simulation runs successfully.


Case II => 6LYZ + water molecules + CL-
            => Gromacs 4.0.5
            => Have tried the correct addition of ions to my .top file
            => The potential energy goes very negative after EM
            => the PR step broke.

Thank you
Lin




Hi Lin,

First of all, I would suggest sticking to a single processor until you
have a protocol that works.
Previously you had an issue with the addition of ions to your .top
file. In your protocol, it's not mentioned. Have you made sure that
issue is cleared?

Cheers,

Tsjerk

On Sun, Jan 10, 2010 at 5:25 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/9/10 10:42 PM, Chih-Ying Lin wrote:
>>
>> Hi
>> I did the EM and the potential energy went to the very negative number.
>> But the simulaiton broke in the PR step.
>> Thank you
>> Lin
>>
>
> Saying the system broke is useless.  There will certainly be some
> information in the .log file (LINCS warnings, etc).  If that is the case,
> then you need to follow the standard advice that is always given in such
> cases:
>
> http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> If you want more detailed advice, provide real output - information from how
> well the EM converged, messages in the .log file (unless it's just LINCS
> stuff, see the above links).  Also realize that EM does not always remove
> all potentially problematic contacts.  Your system may require a bit more
> finesse.
>
> -Justin
>
> --
> ========================================
>