[gmx-users] MD Error after adding a unnatural amio acid

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jan 24 20:21:35 CET 2007

Hi Liu yuemin,

Now I haven't got a clue of what you're trying to do!
Okay, add a new group somewhere and do MD...

First of all, what is the group you're talking about? How did you link
it. You mention the linkage being broken, but you're not doing QM;
bonds stay bonds, but may go well out of bounds. Did you perform
energy minimization? Did you check the stability of the group alone in
You talk about different groups for temperature coupling? Maybe give
the tc_coupl related lines from the .mdp files? Note that you
shouldn't couple such a group separately. Or do you mean charge
groups? Please try to be clear on such things.
Anyway, at this point the partial charges seem to be the least of your
worries (unless you have a collection of -1,+1 or worse stuck
together). I suspect your trouble is related to the building block.



On 1/24/07, yuemin liu <liucan1 at yahoo.com> wrote:
> Hi Everyone,
> I once talked about this before and have new problem
> now. The new group was successfully attached to the
> protein, but problem comes during the process of MD.
> The error messages are always like the following with
> either new linkage broken or a neighboring Hydrogen
> flying away. Parameters except for partial charge are
> perfectly okay. The partial charges from HF
> calculations even made it worse, because of different
> scheme with gmx. I also tried to partition the new
> bulky group into small fragments when T-coupling, but
> did not help. I am wondering what the reasons are. Is
> the new group too big? What is the alternative to
> assign partial charge in gmx other than PRODRG?
> Wishes,
> Liu, Yuemin
>     Energies (kJ/mol)
>            Bond          Angle    Proper Dih.
> Improper Dih.          LJ-14
>     4.40414e+03    7.17452e+03    3.03251e+03
> 2.44614e+03    2.21377e+03
>      Coulomb-14        LJ (SR)   Coulomb (SR)   Coul.
> recip.      Potential
>     4.01788e+04    2.57243e+05   -1.94251e+06
> -2.87497e+05   -1.91331e+06
>     Kinetic En.   Total Energy    Temperature Pressure
> (bar)
>     3.45332e+05   -1.56798e+06    2.99118e+02
> -1.03238e+01
> Shake did not converge in 1000 steps
>     i     mi      j     mj      before       after
> should be
>  3173  14.01   3174   1.01     0.10000     0.15192
> 0.10000
> Constraint error in algorithm Shake at step 650187
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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