Re: GBIS and ABF

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Tue Mar 22 2011 - 18:13:18 CDT

On Tuesday 22 March 2011 23:16:54 Branko wrote:
> Giacomo,
>
> Sorry because a question on CVS version, but I try to combine GBIS and
> ABF (linux CVS-2011-03-20 for Linux-x86_64), and likely that bug exist.
> Simulation works when GBIS without ABF are applied, also when GBIS is
> excluded but ABF applied, simulation works on 2.7 (win), but no on CVS.
> In GBIS and ABF combination, or in "ABF alone" on CVS whole calculation
> were initialized properly, but after that crash, without any "error
> message" in out file
> Please let me know are you try with GBIS and ABF combination in some of
> CVS. I use two colvars, one of which is distance between centroid
> defined on aromatic ring, and some other 'one atom'; second colvar is
> also distance defined on 3 atoms of each of two di-phenyl-methyl
> moieties that molecule comprise (also I try there to overcome any
> symmetry, when centroids are defined,even there is no constraints). BC
> was not applied.
>

Hi Branko,

I am using NAMD CVS-2011-03-03 with GBIS, one dihedral COLVAR and ABF so far
it works fine. Furthermore I use Langevin temperature control and PBC.

GBIS config:

GBIS on
solventDielectric 80
intrinsicRadiusOffset 0.09
ionConcentration 0.3
GBISDelta 1.0
GBISBeta 0.8
GBISGamma 4.85
alphaCutoff 14 cutoff (def:15).

This is my colvars file:

colvarsTrajFrequency 500
colvarsRestartFrequency 500
colvar {
  name eprof conversely,
  
  lowerBoundary -180
  upperBoundary 180

  lowerWallConstant 0.1
  upperWallConstant 0.1
  outputSystemForce no
  outputAppliedForce no

  dihedral {
    group1 {
      # Use only Calpha
      atomnumbers {4 21 38 57 77 93 115 129 148 162 169 191 205 224 238 257
272 288 305 317 328 340 354 373 388 402 418 440 450 472 491 508 520 542 557
564 585 599 611 623 640 657 681 700 719 739 749 756 778 795 814 829 841 848
872 886 905 916 928 949 963 982 999 1021 1036 1047 1061 1080 1097 1116 1132
1151 1175}
    }
    group2 {
      # Use only Calpha
      atomnumbers {1194 1218 1225}
    }
    group3 {
      # Use only Calpha
      atomnumbers {1244 1251}
    }
    group4 {
      # Use only Calpha
      atomnumbers {1268 1285 1304 1324 1340 1362 1376 1395 1409 1416 1438 1452
1471 1485 1504 1519 1535 1552 1564 1575 1587 1601 1620 1635 1649 1665 1687
1697 1719 1738 1755 1767 1789 1804 1811 1832 1846 1858 1870 1887 1904 1928
1947 1966 1986 1996 2003 2025 2042 2061 2076 2088 2095 2119 2133 2152 2163
2175 2196 2210 2229 2246 2268 2283 2294 2308 2327 2344 2363 2379 2398 2422}
    }
  }
}

abf {
  colvars eprof
  fullSamples 100
  hideJacobian no
}

Kind regards,
Bjoern

-- 
Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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