VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Apr 25 2014 - 10:29:15 CDT

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
> <mailto: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
>>
>
>