[gmx-users] gromacs.org_gmx-users Digest, Vol 117, Issue 47

[abhijit Kayal]

doing normal mode analysis in gromacs the starting geometry should be
properly energy minimized. For that you can run in double precision and in
nma.mdp file emtol should be very less. may be 1 or 0.01. when you are
getting eigenfrequency exactly first six eigenfrequency shoul be zero.


On Fri, Jan 17, 2014 at 1:52 PM, Hao Ren <renh.cn at gmail.com> wrote:

> Hi Abhijit,
>
> Thank you for your reply.
>
>
> There is no negative frequencies in the output.
>
> I am just running a test case, a Gly3 (GGG) in a vacuum box, to test
> whether Gromacs can predict reasonable frequencies/normal modes for high
> frequency vibrations.
>
> The configuration, topology and md input files are attached.
>
> I do not know whether I ran a correct simulation with appropriate
> parameters or I just made some mistakes.
>
> Could you please help me to check that?
>
> Many thanks,
> Hao
>
>
>
>
> On Fri, Jan 17, 2014 at 7:56 AM, Hao Ren <renh.cn at gmail.com> wrote:
>
>> >Hi all,
>>> >
>>> >I am trying to do vibrational analysis for some high frequency modes in
>>> >peptides (using force field method), such as the N-H stretching, C=O
>>> >stretching, N-H bending, etc.
>>> >
>>> >However, I got some unreasonable large frequencies, 6,000-250,000
>>> >wavenumbers, which are obviously not correct.
>>> >
>>> >Does anyone has experience on this issue? I just wanna know whether
>>> force
>>> >filed can predict such kind of vibrations with frequencies usually in
>>> the
>>> >range 1,000~3,000 wavenumbers.
>>> >
>>> >I appreciate any help and suggestions,
>>> >Best Regards,
>>> >Hao
>>> >--
>>> >Gromacs Users mailing list
>>> >
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>>> >
>>>
>>
>> -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur
>> ------------------------------ Message: 4 Date: Fri, 17 Jan 2014 10:42:59
>> +0530 From: abhijit Kayal <abhijitchemiitd at gmail.com> To:
>> gmx-users at gromacs.org Cc: gromacs.org_gmx-users at maillist.sys.kth.seSubject: Re: [gmx-users] normal mode analysis for high frequency vibrations
>> Message-ID: <CANu9SWieiJA3Z4yv1Er0V3h=KSmWOhvJRdQTBzzFKRO=Ru2bOA@
>> mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 can you
>> give me more details? Is there any negative frequency you have found?
>>
>
>
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-- 
Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur