Hello,
When you use ntc=1, try also using ntf=1. ntc restrains the bond lengths,
but by setting ntf=2, you are omitting all force calculations involving
hydrogens (bonded force calculations, that is, obviously the non-bonded ones
are still executed).
Hope this helps,
Jason
On Fri, Oct 1, 2010 at 4:30 PM, Kirsten Heitmann <kirstenheitmann.gmx.net>wrote:
> 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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 01 2010 - 14:00:06 PDT
