VMD-L Mailing List

From: Ashish .Chauniyal (ashishchauniyal_at_gmail.com)
Date: Sat Apr 26 2014 - 10:10:45 CDT

I use Fedora Linux, in this, as I said I have 16 cores and 32 gb ram.
At present I am only using half the processors and space, because some
other program is running already. I need to know that is the only cause for
this problem is my Memory or could it be something else as well?

On Sat, Apr 26, 2014 at 8:32 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
> On Apr 26, 2014 10:38 AM, "Ashish .Chauniyal" <ashishchauniyal_at_gmail.com>
> wrote:
> >
> > I have also tried saving the combined file in a .pdb format.
> > combined.pdb
> > It works fine, but am still unable to write the lammpsdata file which
> gives me the same error.
>
> Please make sure you have the latest alpha test version of VMD and the
> up-to-date version of topotools. Also, if you are by chance running on
> windows, all your RAM and CPU cores are not helping you much.
>
> >
> > On Sat, Apr 26, 2014 at 7:31 PM, Ashish .Chauniyal <
> ashishchauniyal_at_gmail.com> wrote:
> >>
> >> Hi Josh,
> >> I tried executing the code line by line, every thing works well except
> >> topo writelammpsdata data.composite atomic
> >>
> >> Also I am not low in memory, I have 16 cores xeon processor, and 32 GB
> ram.
> >> What seems to be the problem??
> >>
> >>
> >> On Fri, Apr 25, 2014 at 8:59 PM, Josh Vermaas <vermaas2_at_illinois.edu>
> wrote:
> >>>
> >>> Hi Ashish,
> >>>
> >>> Segfaults sometimes indicate running out of memory, especially on
> 32-bit systems. If you enter the script line by line into the tkconsole,
> which line causes the problem?
> >>> -Josh
> >>>
> >>>
> >>> On 04/25/2014 06:14 AM, Ashish .Chauniyal wrote:
> >>>>
> >>>> Hi all,
> >>>>
> >>>> In continuation from the last mail, i was able to generate and view
> two .pdb files consisting of two types of atoms only. As Josh had pointed
> I did exactly the same to combine the two files into one.
> >>>> I tried this on a dummy run and it worked , however now when i am
> trying to join to .pdb files consisting of 256000 atoms each, it says
> "Segmentation fault (Core Dumped)"
> >>>>
> >>>> My tcl script looks like this.
> >>>>
> >>>> set solute [mol new leftside.pdb]
> >>>> set solvent [mol new rightside.pdb]
> >>>> set combined [::TopoTools::mergemols "$solute $solvent"]
> >>>> topo writelammpsdata data.composite atomic
> >>>>
> >>>>
> >>>>
> >>>> On Wed, Apr 16, 2014 at 9:34 PM, Josh Vermaas <vermaas2_at_illinois.edu>
> wrote:
> >>>>>
> >>>>> Mergemols takes a list argument. Should be:
> >>>>> set combined [::TopoTools::mergemols [list $solute $solvent]]
> >>>>> -Josh Vermaas
> >>>>>
> >>>>>
> >>>>> On 04/16/2014 10:07 AM, Ashish .Chauniyal wrote:
> >>>>>>
> >>>>>> Dear all,
> >>>>>>
> >>>>>> I have to merge two .pdb files into one and make a lammps data file
> out of it. Please can someone find what am I doing wrong, my TCL console
> says invalid command name "x" this x keeps on changing and I cant pinpoint
> where the error is. Here is the code.
> >>>>>>
> >>>>>>
> >>>>>> #topotools is already included
> >>>>>>
> >>>>>> mol new MG.xyz
> >>>>>> set Cusel [atomselect top "name H"]
> >>>>>> $Cusel set name Cu
> >>>>>> $Cusel set mass 63.54
> >>>>>> set Zrsel [atomselect top "name He"]
> >>>>>> $Zrsel set name Zr
> >>>>>> $Zrsel set mass 91.224
> >>>>>>
> >>>>>> set all [atomselect top "all"]
> >>>>>> $all writepdb leftside.pdb
> >>>>>>
> >>>>>> $all moveby {80.0 0.0 0.0}
> >>>>>> $all writepdb rightside.pdb
> >>>>>>
> >>>>>> #merging the two files
> >>>>>> set solute [mol new leftside.pdb]
> >>>>>> set solvent [mol new rightside.pdb]
> >>>>>> set combined [::TopoTools::mergemols "$solute $solvent"]
> >>>>>>
> >>>>>> $combined writepdb combine.pdb
> >>>>>> topo writelammpsdata data.composite atomic
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> >
>