Am Freitag, den 01.10.2010, 07:55 -0400 schrieb case:
> On Thu, Sep 30, 2010, Kirsten Heitmann wrote:
> >
> > What do you describe is what I have done. In a first step I have removed
> > the charges on the specified atoms than use softcore. This was done
> > without any problems and then I want to add the charges to the specific
> > atoms, and then the problem occurs.
>
> I guessing that we will need to see the input files; try to see if there is
> anything different between the charge removal, (which went OK) and the charge
> adding step. These two steps should be mirrors of each other, using the same
> parameters, and so on.
>
> ....dac
Here is the input file from the problematic one:
mdin_min_s1_v0_l1_dna: (charge removal)
&cntrl
imin = 1, ntx = 1,
maxcyc = 500,
ntpr = 100,
ntf = 2, ntc = 2,
ntb = 1, cut = 12.0,
icfe = 1, clambda = 0.1,
ifsc=0,
crgmask='',
&end
mdin_min_s3_v0_l1_dna: (adding charge)
density minlibration
&cntrl
imin = 1, ntx = 1,
maxcyc = 500,
ntpr = 100,
ntf = 2, ntc = 1,
ntb = 1, cut = 12.0,
icfe = 1, clambda = 0.1,
ifsc=0,
crgmask=':1,10,11,20',
&end
I use ntc=1 because with ntc=2 i got this error-message:
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 110 301 303
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
*** Especially for minimization, try ntc=1 (no shake)
Here the input-files from which went ok:
mdin_min_s1_v0_l2_dna: (charge removal)
density minlibration
&cntrl
imin = 1, ntx = 1,
maxcyc = 500,
ntpr = 100,
ntf = 2, ntc = 2,
ntb = 1, cut = 12.0,
icfe = 1, clambda = 0.2,
ifsc=0,
crgmask='',
&end
mdin_min_s3_v0_l2_dna: (adding charge)
density minlibration
&cntrl
imin = 1, ntx = 1,
maxcyc = 500,
ntpr = 100,
ntf = 2, ntc = 2,
ntb = 1, cut = 12.0,
icfe = 1, clambda = 0.2,
ifsc=0,
crgmask=':1,10,11,20',
&end
So in principal it is the same.
Kirsten
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Received on Fri Oct 01 2010 - 14:00:03 PDT
