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)
>>
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>>
>
>
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Received on Tue Apr 09 2013 - 23:00:03 PDT
