AMBER Archive (2003)

Subject: RE: Residual dipolar couplings

From: McAteer, Kathleen (Kathleen.McAteer_at_pnl.gov)
Date: Wed May 21 2003 - 12:49:18 CDT

Thanks for the prompt reply. A short summary of the energies is shown below. Initally the energies are quite different but they are pretty similar for the first 12 psec of MD. The first vlimit exceeded error appears after step 11643. (vlimit is set to 20). Would it be helpful if I sent you the complete output files?

                E Constraint (6) E Constraint (7) E Align (6) E Align (7)

Step 0 72.06 174.9 71.7 174.5
Step 1 84.43 168.1 47.6 117.2
Step 5 36.03 33.52 7.63 2.41
Step 10 30.59 28.90 1.95 5.29
Step 11 31.34 24.36 4.94 3.26
Step 12 22.22 58.48 3.76 29.61
Step 13 27.07 3749.1 5.12 1461.7
Step 20 38.02 29371.9 23.4 126.9

Thanks!!

Kate

> ----------
> From: David A. Case
> Sent: Tuesday, May 20, 2003 6:25 PM
> To: McAteer, Kathleen
> Subject: Re: Residual dipolar couplings
>
> On Tue, May 20, 2003, McAteer, Kathleen wrote:
>
> > I was wondering if anyone
> > could help me find the problem I am having when I use RDCs in a DNA
> > simulation in AMBER7. I run into a vlimit error after 11 psec of MD and my
> > final energies are huge!
>
> Can you look at just the first few (say 10) steps in both amber6 and amber7?
> Or even just 1 step, to see if the constraint energies (both for the distance
> and angle NMR restraints, and for the dipolar couplings) are the same, or at
> least very close? We want to find out when things start getting a lot
> different, and to try to pin down if the problems are coming from the RDC
> stuff itself, or from some other difference between the two versions.
>
> As far as I know, there is no real improvment for amber7 vs amber7 for this
> type of calculation (let me know if I am forgetting something!). So you
> should be able to continue with the older codes while we get your amber7
> problem sorted out.
>
> We haven't had any other complaints about RDC in version 7, but I don't know
> if people are really using it or not. (I myself haven't done anything
> with that.) So your test case may be very helpful to us.
>
> ..regards....dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
>
>
>