[gmx-users] re K+ ion
Yang Ye
leafyoung81-group at yahoo.com
Thu Jan 19 13:21:52 CET 2006
have a try with a system just with two atoms, Na+ and Cl-.
taveechai taveecharoenkool wrote:
> Dear Yang,
> Thanks again.
> i got this line
> atom[ 52281]={type= 25, typeB= 25, ptype= Atom, m=
> 3.90983e+01, q= 1.00000e+00, mB= 3.90983e+01, qB=
> 1.00000e+00, resnr=13633} grpnrs=[ 3 3 0 0 0 0 0 0 0
> ]}
> which should mean my K+ has +1 charge. and there is no
> NB interaction from
> excl[52281][211661..211661]={52281}. Now , i just
> wonder when i use g_saltbr it doesn't say interaction
> of K+ and CL- ions. My system contains 488 K+ and 488
> CL-.
>
> --- Yang Ye <leafyoung81-group at yahoo.com> wrote:
>
>
>> taveechai taveecharoenkool wrote:
>>
>>> Hi Yang,
>>> I don't understand what you mean, please give me
>>>
>> an
>>
>>> example.
>>> i see
>>> excl:
>>> multinr[division over processors]:
>>>
>> 52414 0
>>
>>> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>> 0 0
>>
>>> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>> 0 0
>>
>>> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>> 0 0
>>
>>> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>> 0 0
>>
>>> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>> 0 0
>>
>>> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>> 0 0
>>
>>> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>> 0 0
>>
>>> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>> 0 0
>>
>>> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>> 0 0
>>
>>> 0 0 0 0 0 0 0 0 0 0 0
>>> nr=52414
>>> nra=211794
>>> excl[0][0..5]={0, 1, 2, 3, 4, 5}
>>> excl[1][6..13]={0, 1, 2, 3, 4, 5, 6,
>>>
>> 18}
>>
>>> excl[2][14..19]={0, 1, 2, 3, 4, 5}
>>> excl[3][20..30]={0, 1, 2, 3, 4, 5, 6,
>>>
>> 7,
>>
>>> 18, 19, 20}
>>> excl[4][31..38]={0, 1, 2, 3, 4, 5, 6,
>>>
>> 18}
>>
>>> what does this mean?
>>> Please help,
>>>
>>>
>> excl[0][0...5] means for atom #0 (find this in your
>> gro file) has 6
>> exclusion respectively to atom #0, #1, #2,...,#5.
>> In your problem, you may locate the atom # for K and
>> find its' exclusion
>> list. Exclusion means there is no NB interaction
>> between the pair.
>> You can also check the charge for K in the dump
>> file.
>>
>>> --- Yang Ye <leafyoung81-group at yahoo.com> wrote:
>>>
>>>
>>>
>>>> use gmxdump -s to check whether there is
>>>>
>> exclusion
>>
>>>> between them (look
>>>> for "excl")
>>>>
>>>> taveechai taveecharoenkool wrote:
>>>>
>>>>
>>>>> Dear Jochen,
>>>>> thanks very much for your reply. Anyway, i
>>>>>
>> already
>>
>>>>>
>>>>>
>>>> did
>>>>
>>>>
>>>>> what you suggest. I can run without the problem.
>>>>>
>> I
>>
>>>>> want to analyze the system after 1ns or 2ns,
>>>>>
>> when
>>
>>>>>
>>>>>
>>>> i
>>>>
>>>>
>>>>> use g_saltbr which tell the oppositely
>>>>>
>> two-charged
>>
>>>>> groups. it doesn't have interaction of K+ and
>>>>>
>>>>>
>>>> negative
>>>>
>>>>
>>>>> charge. I quite don't understand.. where my K+
>>>>>
>>>>>
>>>> charge.
>>>>
>>>>
>>>>> --- Jochen Hub <jhub at gwdg.de> wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> taveechai taveecharoenkool wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Dear all,
>>>>>>> I want to study the effect of K ion on a
>>>>>>>
>>>>>>>
>>>> protein.
>>>>
>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> I
>>>>>>
>>>>>>
>>>>>>
>>>>>>> add this line in ions.itp
>>>>>>> [ moleculetype ]
>>>>>>> ; molname nrexcl
>>>>>>> K+ 1
>>>>>>> [ atoms ]
>>>>>>> ; id at type res nr residu name at name cg nr
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> charge
>>>>>>
>>>>>>
>>>>>>
>>>>>>> mass
>>>>>>> 1 K+ 1 K+ K 1 1 39.0983
>>>>>>> it seems ok, i can run (mdrun) without error.
>>>>>>>
>>>>>>>
>>>> The
>>>>
>>>>
>>>>>>> thing in my mind is that is it enough (to edit
>>>>>>>
>>>>>>>
>>>> only
>>>>
>>>>
>>>>>>> one file) cos it seems like K+ doesn't contain
>>>>>>> positive charge when i used g_saltbr? i use
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> Gromos96
>>>>>>
>>>>>>
>>>>>>
>>>>>>> forcefield.
>>>>>>> Thanks in advance
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> You should add a
>>>>>> K+ 1
>>>>>>
>>>>>> into the [ molecules ] section of your
>>>>>>
>> topol.top.
>>
>>>>>> And , of course, you need to place it into your
>>>>>> starting structure (pdb
>>>>>> or gro).
>>>>>>
>>>>>> Jochen
>>>>>>
>>>>>> --
>>>>>>
>>>>>>
>> ************************************************
>>
>>>>>> Jochen Hub
>>>>>> Max Planck Institute for Biophysical Chemistry
>>>>>> Computational biomolecular dynamics group
>>>>>> Am Fassberg 11
>>>>>> D-37077 Goettingen, Germany
>>>>>> Email: jhub[at]gwdg.de
>>>>>>
>>>>>>
>> ************************************************
>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>> __________________________________________________
>>
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>>>>>
>>>>>
>>>>>
>>>> --
>>>> /Regards,/
>>>> Yang Ye
>>>> /Computational Biology Lab
>>>> School of Biological Sciences
>>>> Nanyang Technological University
>>>> Singapore
>>>> Tel: 6316-2884
>>>> /
>>>>
>>>>
>>>>
>>> __________________________________________________
>>>
> === message truncated ===
>
>
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--
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/
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