Re: GBIS and ABF

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Wed Mar 23 2011 - 07:04:29 CDT

I forgot to mention, that I always use the charm snapshot when i compile NAMD.
http://charm.cs.uiuc.edu/autobuild/bin/charm_src.tar.gz

Cheers,
Bjoern

On Wednesday 23 March 2011 11:01:14 Branko wrote:
> Hi Bjoern,
>
> Thank you very much for respond. Yes I also use Langevin temperature,
> and input for both GBIS and ABF are similar to your, still something
> wrong happened. Please let me know about size of your system, also are
> colvarsRestartFrequency same as MD restart. Below are my inputs
>
> Kind regards
>
> Branko
>
>
> ____
>
> small molecule in implicit EtOH
>
> #GBIS parameters
> GBIS on
> solventDielectric 24.3
> ionConcentration 0
> intrinsicRadiusOffset 0.09
> GBISDelta 1.0
> GBISBeta 0.8
> GBISGamma 4.85
> alphaCutoff 14
>
> # Other parameters
> colvars on
> colvarsConfig Hmd
>
> ___
> ABF
>
>
> colvarsTrajFrequency 1
> colvarsRestartFrequency 10000
> analysis on
>
>
> colvar {
> name distance
> lowerBoundary 3.40
> upperBoundary 12.20
> width 0.01
>
> distance {
> group1 {
> atomnumbers 1 16 17
> }
> group2 {
> atomnumbers 36
> }
> }
> }
>
> colvar {
> name distance2
> lowerBoundary 4.80
> upperBoundary 12.20
> width 0.01
>
> distance {
> group1 {
> atomnumbers 18 19 20 21
> }
> group2 {
> atomnumbers 22 23 24 25
> }
> }
> }
>
>
> abf {
> colvars distance distance2
> fullSamples 500
> hideJacobian no
> outputFreq 1000
> applyBias yes
> }
>
> On 3/23/2011 12:13 AM, Bjoern Olausson wrote:
> > 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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