Re: AMBER: Vlimit problem

From: Thomas E. Cheatham, III <>
Date: Fri, 9 Jan 2004 14:53:10 -0700 (Mountain Standard Time)

I don't remember if other's replied to this, but...

> I have encountered a problem with vlimit when runing the simulation of an unmodified control of a 11mer
> B - DNA with 20 Na+ counterions added and waterbox of 10 A in each dimension. I set vlimit=15.0 for the
> second step "dynamics holding the solute fixed",after 1000 steps of steepest descent minimization and
> 4000 steps of conjugate gradient minimization. The output file indicates that vlimit is exceeded. I
> follow the example form the tutorial. How is the value in the example shown in the tutorial chosen? Can

The tutorial is somewhat out-of-date and should be tweaked.

> I possibly enlarge the vlimit to 20.O? Attached are the output files. Any suggestions?

Increasing vlimit is perfectly reasonable. The presence of the vlimit
flag is to both (a) warn of instability and (b) truncate random high
forces. If they repeatedly occur, this is evidence of an underlying
stability and is usually related to (1) strong overlap of atoms or (2)
vibrational frequencies that are faster than the integrator can handle.

In this case, it is likely the fact that the NTR=1 force constant is 500.0
kcal/mol which is a too large (bond) force constant. This leads to much
to fast vibration or very large restoring forces that lead to the vlimit
problem. When the tutorial was originally run (a long time ago), vlimit
was not implemented (or defaulted to a higher value).

A much more reasonable force constant is in the 5.0 range or even 2.0.
This will be enough to hold the solute in place.

> And another question, is it possible to change the random number seed card "IG" to get a better results

Changing the seed will not give "better" results, just different results.
As you are seeing a systematic error (i.e. too large force constant)
rather than random error, changing the seed will not help.

> If so what's the algorithm to get other random numbers ? And should I
> keep the same IG for the whole run of dynamics ?

IG as a seed ONLY has an effect when the initial velocities (unless you are doing NTT=4 or VRAND).

Let me know directly if reducing the force constant doesn't solve the


\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
| (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418

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Received on Wed Jan 14 2004 - 15:53:15 PST
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