[gmx-users] NVT.mdp equilibration problem

[fsaadedi at staffmail.ed.ac.uk]

Dear Anton,

Thanks for your advice, I will check my pdb and see if there are any bad
contacts.

Farid

Quoting Anton Feenstra <feenstra at few.vu.nl>:

> fsaadedi at staffmail.ed.ac.uk wrote:
>
>> Dear fellow users,
>>
>> I have been trying to equilibrate my DOPC bilayer using an NVT ensemble for
>> 100ps.  Unfortunately the equilibration crashes after just 1.5ps.  
>> It crashes
>> because several bonds rotated more than 30 degrees.  I have tried 
>> contraining
>> my bonds all-bonds, hbonds and none with no effect.  If anyone has any
>> suggestions I would appreciate them.
>
>
> Check your starting configuration - there are almost certainly some 
> bad atomic clashes somewhere. Start off by looking at (and around) 
> those atoms that had the LINCS warnings.
>
> -- 
> Groetjes,
>
> Anton
>
> * NOTE: New Affiliation, Phone & Fax numbers (below) *
>  _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam   |
> |(   |   )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands  |
> | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
> |             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
> |             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
> |_____________|_______________________________________________________|
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
>