VMD-L Mailing List

From: Ashish .Chauniyal (ashishchauniyal_at_gmail.com)
Date: Sat Apr 26 2014 - 09:07:27 CDT

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.

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
>>>
>>>
>>>
>>
>>
>