Re: AMBER: restraint value: written but none specified

From: Ben Sattelle <>
Date: Fri, 20 Apr 2007 23:08:55 +0100

thanks for the prompt reply,

yes, the non-zero restraint is printed at every step, each ps in this case.
interestingly, the restraint is also non-zero in the next, restarted,
production phase of the simulation where, again, ntr=0 ...

production at 300K, 100ps, 1fs step, shake, npt











again, diff'ing the production input files from this and previous
'RESTRAINT=0.0' production runs yeilds no difference, as if the discrepency
derives from the prmtop / inpcrd / rst files. the only observable
difference is
the existance of a `Water cap` section in the output containing non-zero
restraint values ...

Water cap:
     ivcap = 0, natcap = 15640
     fcap = 1.50000, cutcap = 3.00000
     xcap = 17.79550, ycap = -3.11100, zcap = 0.65500

perhaps I am misusing solvatecap (ref. previous email). I am using Amber9, I
suspect this will affect the free energy values I am interested in? Ben.

> On Fri, Apr 20, 2007, Ben Sattelle wrote:
>> output includes a restraint value although none were specified (ntr=0),
> Assuming you have no "nmr" restraints, or "targetted" restraints,
> this indeed looks odd.
>> `EAMBER (non-restraint)` and `RESTRAINT` values have not been written
>> for previous runs using this input
> Can you find out what changed between "this run" and "previous runs"?
> Is the non-zero restraint printed at all steps, or only at step 10000?
> RESTRAINT should always be printed, although the value might be zero.
> "non-restraint" is only printed when RESTRAINT is non-zero, so that
> part makes
> sense.
> You may have to play around with different input combinations to see what
> is going on. Also, let us know what version of Amber you are using.
> ....good luck...dac
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Received on Sun Apr 22 2007 - 06:07:49 PDT
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