Re: [AMBER] problem setting drms to low values

From: Attilio Vittorio Vargiu <attilio.vargiu.gmail.com>
Date: Mon, 5 Dec 2011 14:52:21 -0800

Dear Prof. Case,
thank you for your suggestion, I modified the input to just restraint
a selection of residues, but now I am facing another problem.
In the output I get the following error:

Error in group input::atommask.f::pop_evalstack
stack underflow

I tried increasing the maxstack parameter to 768 and later 2560
(originally was 256)
in routine findmask, and the max_finds to 1000 in rgroup.f, but again
I probably missed the right one. I tried changing these parameters
because if I stop to resid 252 in restraintmask (see below), sander works,
and this corresponds to 256 characters in the string.
Below is the input, any suggestion would be more than welcomed.

Thanks,
Attilio

try again...
&cntrl
ntxo = 1,
ntf = 1, ntb = 0, ntr = 1,
dielc = 1,
cut = 999.0, nsnb = 99999,
imin = 1, ntmin=3, maxcyc = 100000,
ncyc = 0, drms = 0.0000000001,
restraint_wt=10.0,
restraintmask=':1-11,16-19,21-26,28,30-31,40-54,62,65,74-76,84-87,92-93,95-101,105-111,120,123-125,130-132,134,139,140,142-147,149-151,153-154,157-159,163-165,169,172,175-179,182,187,189,192-194,196,202,204-208,211,215,216,219,222-225,227,229,234,236,239-242,244-248,252,254,256,259,265,266,271,272,275,276,278,280,283-287,290,297-301,304-306,308-319,322-323,328,329,331,334,336,337,339,341-343,345-347,350,352,353,355,356,361,364'
/



2011/12/5 David A Case <case.biomaps.rutgers.edu>:
> On Sat, Dec 03, 2011, Attilio Vittorio Vargiu wrote:
>
>> Essentially I want to perform a tough optimization to perform nm analysis,
>> so I put a drms value of 10-10 in the input.
>
> I don't think you can use the belly option and still get very low gradients.
> The belly option just zeroes the forces on certain atoms, which violates
> the smoothness criteria needed for the minimizer. If you need to keep certain
> atoms fixed, use ntr=1 instead.
>
> ...dac
>
>
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-- 
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         Attilio Vittorio Vargiu, PhD
 SLACS & Department of Physics, University of Cagliari
 Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700
       09042 Monserrato (CA), Italy
      e-mail1: vargiu.dsf.unica.it
      e-mail2: attilio.vargiu.gmail.com
      Phone: +390706754847
      Fax: +39070510171
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Received on Mon Dec 05 2011 - 15:00:03 PST
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