Hi Daniel,
I think I got the reason for the message - " FYI: NEVEC > NELEM: Number of
calculated evecs were reduced to 260 ". This is probably because of the
number of vectors mention with the 'analyze' (vecs 293) is greater the the
actual number vectors calculated, which in 260.
Thanks and Regards
Anu
On Wed, Apr 10, 2013 at 11:11 AM, anu chandra <anu80125.gmail.com> wrote:
> Hi Daniel,
>
> Here the input file I used for the calculation.
>
> ***********************************************************
> trajin ../9md.crd
> trajin ../10md.crd
> trajin ../11md.crd
>
>
> center :1-293 mass origin
> image origin center
>
> reference ../leap.pdb
>
> rms reference mass :1-293
>
>
> vector v2 :2.CB ired :2.CG
> vector v3 :3.CB ired :3.CG2
> vector v4 :4.CB ired :4.CG
> vector v5 :5.CB ired :5.CG
> vector v6 :6.CB ired :6.CG
> vector v7 :7.CB ired :7.CG
> ........................
> .......................
> vector v260 :260.CB ired :260.CG
>
>
> matrix ired name matired order 2
>
> analyze matrix matired order vecs 293 out ired_CB_CG.vec orderparamfile
> S2_CB_CG.dat
>
> **************************************************************
>
>
>
>
>
> On Wed, Apr 10, 2013 at 10:34 AM, anu chandra <anu80125.gmail.com> wrote:
>
>> Hi Daniel,
>>
>> I have used 6 vectors just for a trial run. This time I have used all the
>> 260 vectors for the calculation ( Even though the protein have 293
>> residues, I have consider 260 vectors for calculation since I am
>> calculating the order parameters for CB-CG vector). I used 30,000 frames
>> for the calculation. Even though the calculation went successfully with
>> outputting order parameters for all 260 vectors, after the calculation I
>> got a message in the terminal that says " FYI: NEVEC > NELEM: Number of
>> calculated evecs were reduced to 260 ". What does this message means?
>>
>>
>> Thanks in advance
>>
>> Regards
>> Anu
>>
>>
>> On Tue, Apr 9, 2013 at 8:28 PM, Daniel Roe <daniel.r.roe.gmail.com>wrote:
>>
>>> Hi,
>>>
>>> On Tue, Apr 9, 2013 at 12:40 AM, anu chandra <anu80125.gmail.com> wrote:
>>> > Thanks for the reply. Now, as a trial run if I do with 6 vectors, I can
>>> > able to get the S2 order parameter, which seems to be reliable. Here
>>> is the
>>>
>>> Unless you have a specific reason for only using 6 vectors, I really
>>> do recommend that you define a vector for every N-H bond in your
>>> system for this calculation; the more information you have the more
>>> accurate the calculation will be.
>>>
>>> -Dan
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe, PhD
>>> Department of Medicinal Chemistry
>>> University of Utah
>>> 30 South 2000 East, Room 201
>>> Salt Lake City, UT 84112-5820
>>> http://home.chpc.utah.edu/~cheatham/
>>> (801) 587-9652
>>> (801) 585-9119 (Fax)
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
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Received on Tue Apr 09 2013 - 23:00:04 PDT
