VMD-L Mailing List

From: Ashish .Chauniyal (ashishchauniyal_at_gmail.com)
Date: Sat Apr 26 2014 - 09:01:14 CDT

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
>>
>>
>>
>
>