[gmx-users] Help! LINCS WARNING &errors.

SUN, Jian sunjian.nku at gmail.com
Sun Jun 4 16:21:53 CEST 2006

Dear Dr. David van der Spoel,

Thanks for your reply.

1. I didn't set conservation for energy, nor p_couple for my system.
2. You said "bad structures", Do you mean my system is not fully
equilibrium? Or my protein structure is totally wrong? I am trying to
spend more simulation time on equilibrium for the system, will it

I searched the mail list archives for simulated annealing. But there
are so many mails on this topic and most of them are not replied or
solved. Maybe we should have some volunteer to classify the archives
and update the FAQ.  That would be very helpful for newbies like me.

Thanks & Regards,

>SUN, Jian wrote:
> Dear all,
> I am running simulated annealing for a protein in water and found
> something strange:
> 1. the poteintial energy keep on rising while the system is cooling down
conservation of energy?

> 2. several LINCS WARNINGs are given (I have posted the question but no
> reply till now) and then the energies become "nan"
bad structures. check mailing list archives.

> Who can tell me why?
> Thanks a lot.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se

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