[gmx-users] Elastic network model
mohan maruthi sena
maruthi.sena at gmail.com
Fri Aug 31 20:42:47 CEST 2012
Hi all,
I have built topology for elastic network as follows(the
atoms which fall with in a distance less than 6 angtroms are bonded).
[bonds]
;ai aj funct bo kb
2 1 1 3.80444752888 61.9
3 1 1 5.10184956658 61.9
3 2 1 3.69916125628 61.9
4 1 1 4.19781502689 61.9
4 2 1 5.90237528458 61.9
4 3 1 3.92569102197 61.9
5 1 1 5.30324730708 61.9
5 3 1 5.2694262496 61.9
5 4 1 3.83092403997 61.9
6 3 1 4.07288043036 61.9
6 4 1 5.48720921781 61.9
6 5 1 3.71358990735 61.9
7 3 1 5.51608248669 61.9
7 6 1 3.8682865716 61.9
8 7 1 3.8047721351 61.9
9 8 1 3.81975719124 61.9
10 9 1 3.72026195314 61.9
11 10 1 3.76893910802 61.9
12 11 1 3.8123865229 61.9
13 12 1 3.78850801768 61.9
14 13 1 3.69171193351 61.9
15 13 1 5.42834818338 61.9
15 14 1 3.83449357804 61.9
16 13 1 5.10757946585 61.9
16 15 1 3.83922544272 61.9
17 11 1 5.71881902144 61.9
17 12 1 4.83263696133 61.9
17 13 1 5.48196032456 61.9
The above one is part of topology file. I have 372 residues in my
protein. when i run equilibration i got the following error
A list of missing interactions:
Bond . of 1027 missing 1
-------------------------------------------------------
Program mdrun_d, VERSION 4.5.5
Source code file: domdec_top.c, line: 173
Software inconsistency error:
Some interactions seem to be assigned multiple times
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors.
None of the interactions are repeated multiple times, when i check the
log file the following error is written
Not all bonded interactions have been properly assigned to the domain
decomposition cells
A list of missing interactions:
Bond. of 1027 missing 1
-------------------------------------------------------
Program mdrun_d, VERSION 4.5.5
Source code file: domdec_top.c, line: 173
Software inconsistency error:
Some interactions seem to be assigned multiple times
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Error
Can you suggest me what does this error mean . Is the topology correct
(built) with respect to elastic network model.
Thank you,
Mohan
On Thu, Aug 30, 2012 at 5:58 PM, mohan maruthi sena
<maruthi.sena at gmail.com> wrote:
> Hi ,
> Thank you very much .I will take all these factors in to
> account while building the model.
>
> Thank you,
> Mohan.
>
> On Thu, Aug 30, 2012 at 5:53 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>> On 30/08/2012 10:17 PM, Mark Abraham wrote:
>>>
>>> On 30/08/2012 10:02 PM, mohan maruthi sena wrote:
>>>>
>>>> Hi,
>>>> I am going through it , i will understand it and try to build
>>>> the topology.
>>>
>>>
>>> Fundamentally, harmonic bonds do not serve your purpose, since you need an
>>> interaction that is harmonic in the change in distance, not harmonic in the
>>> distance. Hence your problems with collapsing systems. As such, you want to
>>> look at using distance restraints, rather than [bonds].
>>
>>
>> On second thoughts, a sufficient network of harmonic bonds can suffice, but
>> you need to embed the distance in the topology. [distance_restraints] are
>> just easier because you can let the initial structure determine the
>> equilibrium position. (Unless you don't want that)
>>
>> Mark
>>
>>
>>>
>>> Mark
>>>
>>>> Thank you,
>>>> Mohan
>>>>
>>>> On Thu, Aug 30, 2012 at 5:12 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
>>>> wrote:
>>>>>
>>>>> Hi Mohan,
>>>>>
>>>>> You need to check chapter 5 of the gromacs manual to understand the
>>>>> topology format to write. You probably need only to define one atom
>>>>> type and the C6/C12 parameters could probably even be set to zero. You
>>>>> need to write an [ atoms ] section, and a [ bonds ] section, according
>>>>> to the specifications in the manual.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Tsjerk
>>>>>
>>>>> On Thu, Aug 30, 2012 at 1:32 PM, mohan maruthi sena
>>>>> <maruthi.sena at gmail.com> wrote:
>>>>>>
>>>>>> Hi,
>>>>>> Thanks for a quick reply. In these models we use a distance
>>>>>> cut-off method. Around a particular atom we take a cut-off distance
>>>>>> and connect to all those atoms which fall in the cut-off. I do not
>>>>>> understand, how to connect this atoms with the other atoms falling in
>>>>>> cut-off distance. I have written a script to know the atom numbers
>>>>>> falling with in cut-off distance. I replace bonds section in topology
>>>>>> with these atom connectivity information that i got from script. Is
>>>>>> this method correct or else please suggest me a way.Can you elaborate
>>>>>> on "write a script to generate .top"
>>>>>>
>>>>>>
>>>>>> Thank you very much,
>>>>>> Mohan
>>>>>>
>>>>>> On Thu, Aug 30, 2012 at 3:18 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
>>>>>> wrote:
>>>>>>>
>>>>>>> Hi Mohan,
>>>>>>>
>>>>>>> Elastic network modeling consists of building a Hessian matrix based
>>>>>>> on the distances. That matrix is then diagonalized and the modes are
>>>>>>> further investigated. You could write a script to generate a .top file
>>>>>>> with a [ bonds ] section, capturing the elastic bonds, and then use
>>>>>>> Gromacs to generate the Hessian using the nm integrator. But that
>>>>>>> seems more trouble than it's worth. If you think of building such a
>>>>>>> model and then simulate it using an md integrator, be warned that
>>>>>>> these models are very incomplete and are intended to only capture the
>>>>>>> tangents around the starting structure.
>>>>>>>
>>>>>>> Hope it helps,
>>>>>>>
>>>>>>> Tsjerk
>>>>>>>
>>>>>>> On Thu, Aug 30, 2012 at 9:22 AM, mohan maruthi sena
>>>>>>> <maruthi.sena at gmail.com> wrote:
>>>>>>>>
>>>>>>>> Hi all,
>>>>>>>> Can any one suggest me how to build elastic network
>>>>>>>> model
>>>>>>>> in gromacs.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Mohan
>>>>>>>> --
>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Tsjerk A. Wassenaar, Ph.D.
>>>>>>>
>>>>>>> post-doctoral researcher
>>>>>>> Molecular Dynamics Group
>>>>>>> * Groningen Institute for Biomolecular Research and Biotechnology
>>>>>>> * Zernike Institute for Advanced Materials
>>>>>>> University of Groningen
>>>>>>> The Netherlands
>>>>>>> --
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>>>>>>
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>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Tsjerk A. Wassenaar, Ph.D.
>>>>>
>>>>> post-doctoral researcher
>>>>> Molecular Dynamics Group
>>>>> * Groningen Institute for Biomolecular Research and Biotechnology
>>>>> * Zernike Institute for Advanced Materials
>>>>> University of Groningen
>>>>> The Netherlands
>>>>> --
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>>
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