VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Aug 13 2012 - 04:38:46 CDT

List added, sorry for previous mail

On Mon, Aug 13, 2012 at 11:22 AM, Francesco Pietra
<chiendarret_at_gmail.com> wrote:
> On Mon, Aug 13, 2012 at 10:37 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>> francesco,
>>
>> On Mon, Aug 13, 2012 at 9:34 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>>> Hi all:
>>> I used often the latest VMD on Linux to evaluate correctly the charge
>>> on a system as indicated by the output below. In contrast, for systems
>>> having lysine protonated at the side chain (-NH3), I am getting charge
>>> zero, while there is no neutralizing negative charge on the system.
>>> Thus I tried with the minimal system of lysine capped with ACE and
>>> NME:
>>>
>>>
>>> Main console display active (Tcl8.5.6 / Tk8.5.6)
>>> (ACE_LYS_NME) 1 % set everyone [atomselect top all]
>>> atomselect0
>>>>Main< (ACE_LYS_NME) 2 % puts "TOTAL CHARGE ON THE SYSTEM: [eval vecadd [$everyone get charge]]"
>>> TOTAL CHARGE ON THE SYSTEM: 0.0
>>>>Main< (ACE_LYS_NME) 3 %
>>>
>>> When the above system is subjected to ab initio calculation - by any
>>> code - the charge has to be set to +1.
>>>
>>> Thanks for advice
>>
>> with classical MD, you get out what you put in.
>> if your system has not the correct charge, then
>> your topology/parameter file is incorrect.
>> VMD can only use the information that you provide.
>
> Axel: I don't understand what you mean. I am not dealing with MD,
> rather with ab initio, and DFT, calculations. Just drawn a system - as
> above - collected the Cartesian coordinates, and subjected to the ab
> initio, or DFT, code. Correctly when the charge is set to +1. I
> thought that VMD, with the above script, reports the charge correctly.
> I must be misusing VMD, or I am completely out the way.
>
> thanks
> francesco
>
>
>>
>> GI-GO
>>
>> axel
>>
>>
>>>
>>> francesco pietra
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.