Dear Amber-users,
1) I have a question about measuring three principal moments of inertia
(Iz, Iy,
Ix). I tried ptraj like below.
-----------------------------------------
trajin test.mdcrd
matrix mwcovar name eigen :1-9
analyze matrix eigen out eigen.xvg vecs 0
------------------------------------------
And then, I got a result below.
------------------------------
Eigenvector file: MWCOVAR
15420 15420
42.16758 59.33372 55.77352 42.72626 59.60342 55.58084 42.53161
59.14592 55.01900 42.50538 58.95597 54.86263 42.44377 58.98121
:
:
---------------------------
Are those numbers eigenvalues? I would like to know how to see and
visualize(in
xmgrace) Ix, Iy, Iz.
2) When I tried same thing second time, I got an error like below.
-------------------------
:
PTRAJ: matrix mwcovar name eigen :1-9
Mask [:1-9] represents 5140 atoms
ERROR in safe_malloc: Error in alloc of 951290640 bytes
--------------------------
Could you tell me how to handle this problem?
best,
Hwankyu.
Quoting Hwankyu Lee <leehk.umich.edu>:
> Thanks for the answers, but have another question about this.
> I simply used analin like below, but I may be able to get only moment of
> intertia (I).
> How can I get three principal moments of inertia (Iz, Iy, Ix) ??
> Before measuring them, do I need to reposition the solutes based on center of
> mass?
>
> --------------------
> FILES_IN
> PARM p1 test.prmtop;
> STREAM s1 test.mdcrd;
> FILES_OUT
> TABLE t1 momin.tab;
> DECLARE
> GROUP grpid1 (RES 1,2,3,4,5,6,7,8,9);
> OUTPUT
> TABLE t1 grpid1%momin;
> END
> ---------------------
>
> best,
> Hwankyu.
>
>
> Quoting Bill Ross <ross.cgl.ucsf.edu>:
>
>>> 1) I would like to see the graph of mass densities or electron
>>> densities of some solutes and solvent across the system box (distance).
>>> I searched ptraj or carnal for this analysis, but couldn't find that.
>>> How can I measure that by using ptraj or carnal?
>>
>> Carnal doesn't do this, not sure about ptraj.
>>
>>>
>>> 2) I know that I can measure moment of inertia by using carnal
>>> (groupid%momin). But, I'm wondering if I can do that in ptraj. How can
>>> I measure moment of inertia by using ptraj?
>>>
>>> 3) When I use ptraj, I know that I can specify analysis intervals by
>>> doing "trajin *** 100 200 1" (from 100ps to 200ps). But, how can I
>>> specify analysis intervals in CARNAL?
>>
>> In carnal you could select the frames you want using OUTPUT COORD SELECT,
>> creating a new trajectory file, then analyze that.
>>
>> However I suggest not using carnal as it will be discontinued.
>>
>> Bill
>>
>>>
>>> Thanks for your help in advance.
>>>
>>> best,
>>> Hwankyu.
>>>
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>>
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Received on Tue May 31 2005 - 05:53:01 PDT
