Re: [AMBER] problem setting drms to low values

From: Attilio Vittorio Vargiu <attilio.vargiu.gmail.com>
Date: Wed, 7 Dec 2011 11:15:48 -0800

Dear all,
do you have some suggestion about the query I made a few days ago?
Any suggestion (even bad words) is welcomed!

Thanks in advance,
Attilio

2011/12/5 Attilio Vittorio Vargiu <attilio.vargiu.gmail.com>:
> 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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>
>
>
> --
> いいいいいいいいいいいいいいいいいいいいいいいいいいいいい
> 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
> いいいいいいいいいいいいいいいいいいいいいいいいいいいいい



-- 
いいいいいいいいいいいいいいいいいいいいいいいいいいいいい
         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
いいいいいいいいいいいいいいいいいいいいいいいいいいいいい
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Received on Wed Dec 07 2011 - 11:30:03 PST
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