Re: GBIS and ABF

From: Bjoern Olausson (bjoern.olausson_at_biochemtech.uni-halle.de)
Date: Wed Mar 23 2011 - 06:57:32 CDT

My "colvarsRestartFrequency" and "colvarsTrajFrequency" are both set to 500
which is identical to my "restartFreq", "dcdfreq" and "xstFreq" setting.

The main difference is your "ionConcentration" (0 vs. 0.3) and colvars
"dihedral" vs. "distance"

My system is a Protein with 2440 Atoms (149 Residues).

You might want to rule out those to differences. If it still crashes for you
it might be a bug in you cvs snapshot?

I'll run my system with a snapshot I'll download NOW ;-)

By the way:
Is it possible to pass arguments (variables) from the namd config to the
colvars config. Lets say I define "set A 200" in the main namd config file can
I somehow use $A in my colvars config file? Simply using $A does not work :-(

Cheers,
Bjoern

On Wednesday 23 March 2011 11:01:14 you 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-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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