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
&cntrl
imin=0,
ntr=0,
nstlim=100000,
nscm=1000,
ntx=5,
irest=1,
ntb=2,
ntp=1,
ntt=1,
taup=2.0,
tautp=2.0,
temp0=300.0,
tempi=300.0,
dt=0.001,
nrespa=1,
ntc=2,
ntf=2,
noshakemask=":ox",
ntpr=1000,
ntwx=1000,
ntwe=1000,
ntwr=1000,
ntave=1000,
cut=9.0,
icfe=1,
clambda=0.00000,
klambda=1,
/
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
