VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Apr 26 2014 - 10:02:00 CDT

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