On 5/04/2011 3:57 PM, ahmet yıldırım wrote:
Dear Tsjerk,
Hi Ahmet,
As suggested, it's better to break up your molecule into smaller
charge groups. Note that charge groups don't need to have zero charge,
nor integer charge. In your case, I'd suggest two COH groups for EDO,
Dear Mark,
Now, are the files correct?
*EDO.itp*:
[ moleculetype ]
; Name nrexcl
EDO 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1OA 1 EDO OAB 1 -0.111 15.9994
2 H 1 EDO HAE 10.031 1.0080
3
On 5/04/2011 9:59 PM, ahmet yıldırım wrote:
Dear Mark,
Now, are the files correct?
They're well-formed, but you've not taken Tsjerk's advice and arranged
for (COH)3(NH3+)C to have charges consistent with its symmetry. When
people donate their time to you, please use it or demonstrate why
Dear Tsjerk,
Hi Ahmet,
As suggested, it's better to break up your molecule into smaller
charge groups. Note that charge groups don't need to have zero charge,
nor integer charge. In your case, I'd suggest two COH groups for EDO,
which will have zero net charge each, and for TRS I'd take the
Dear users,
Before energy minimization step , I performed the preprosessing step using
grompp .
However, there are two note that :
*NOTE 1 [file topol.top, line 52]:*
System has non-zero total charge: -1.50e+01
*NOTE 2 [file topol.top]:*
The largest charge group contains 11 atoms.
Hi Ahmet,
As suggested, it's better to break up your molecule into smaller
charge groups. Note that charge groups don't need to have zero charge,
nor integer charge. In your case, I'd suggest two COH groups for EDO,
which will have zero net charge each, and for TRS I'd take the COH
groups as
On 31/03/2011 5:18 PM, ahmet y?ld?r?m wrote:
Dear users,
Before energy minimization step , I performed the preprosessing step
using grompp .
However, there are two note that :
*_NOTE 1 [file topol.top, line 52]:_*
System has non-zero total charge: -1.50e+01
This is an integer. See
Dear Tsjerk,
I will ask you one thing but please do not get angry (I know you are not a
private tutor but I need your helps).
How do I apply on the files (EDO.itp and TRS.itp) that you said? (or can you
suggest a tutorial?)
Thanks
2011/3/31 Mark Abraham mark.abra...@anu.edu.au
On 31/03/2011
On 31/03/2011 6:17 PM, ahmet yıldırım wrote:
Dear Tsjerk,
I will ask you one thing but please do not get angry (I know you are
not a private tutor but I need your helps).
How do I apply on the files (EDO.itp and TRS.itp) that you said? (or
can you suggest a tutorial?)
You'll need to
Hi Ahmet,
Why would I get angry? :) Sending a reply to the list will not usually
be taken as asking for private tutoring...
As Mark pointed out, you need to get familiar with the format of the
files. That's the first thing you should do if you get to the point of
needing to use non standard
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