VMD-L Mailing List

From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Wed Apr 20 2016 - 09:53:13 CDT

Dear all,

I finally discover the problem. In VMD I was trying to read frame 0,
instead of 1! Now it works!
Even with this stupid error I'm glad I wrote to the list because the
inclusion of the line
molinfo top set {a b c} {0 0 0}
when I have no periodic box information in the dcd file is essential!
Thanks everyone for your answers, specially Jerome.
Best,

Laura

2016-04-19 11:17 GMT+02:00 Laura Joana <laurajoanalopes_at_gmail.com>:

> Hello Giacomo,
>
> That's true, it's always going to be differences. But, calculating the
> dihedral angles with this coordinates they give the same values, with
> slightly differences, evidently. But as I calculate then with VMD they are
> different. That's the problem!
> Best,
>
> Laura
>
> 2016-04-19 0:20 GMT+02:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
>
>> Hi, VMD reads all files and stores them in memory in single precision,
>> thus atomic coordinates cannot be compared to their NAMD counterparts with
>> full digits.
>>
>> Giacomo
>>
>> On Mon, Apr 18, 2016 at 10:05 AM, Laura Joana <laurajoanalopes_at_gmail.com>
>> wrote:
>>
>>> I obtain close values, but they are not exactly equal:
>>> NAMD
>>> -7.75349182128906e+02 -7.74708642578125e+03 2.05269702148438e+03
>>> -7.74688653758182e+02 -7.74826807202096e+03 2.05239478592227e+03
>>> -7.74603393652299e+02 -7.74890428783011e+03 2.05105687624320e+03
>>> -7.75804016113281e+02 -7.74978466796875e+03 2.05070825195312e+03
>>> -7.77042909993649e+02 -7.74924461376854e+03 2.05071753160505e+03
>>>
>>> VMD
>>> {-775.3491821289063 -7747.08642578125 2052.697021484375}
>>> {-774.6886596679688 -7748.26806640625 2052.394775390625}
>>> {-774.6033935546875 -7748.904296875 2051.056884765625}
>>> {-775.8040161132813 -7749.78466796875 2050.708251953125}
>>> {-777.0429077148438 -7749.24462890625 2050.717529296875}
>>>
>>> But it's strange to thing that this slightly difference will cause such
>>> a big difference in the dihedral values... Do you think the problem is here?
>>>
>>> 2016-04-18 15:40 GMT+02:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>>>
>>>> Can you add the following colvar to your config, and then check its
>>>> value against the Cartesian coordinates of those atoms (you can get those
>>>> in VMD):
>>>>
>>>> colvar {
>>>> name xyz
>>>> cartesian {
>>>> atoms {atomNumbers 5 7 9 15 17}
>>>> }
>>>> }
>>>>
>>>> Jerome
>>>>
>>>> On 18 April 2016 at 15:31, Laura Joana <laurajoanalopes_at_gmail.com>
>>>> wrote:
>>>>
>>>>> Jerome,
>>>>> Does it help if I send you the output I'm obtaining with NAMD?
>>>>> Best,
>>>>> Laura
>>>>>
>>>>> 2016-04-18 15:24 GMT+02:00 Laura Joana <laurajoanalopes_at_gmail.com>:
>>>>>
>>>>>> I just got the compiled version (linux x86_64) and I got the same
>>>>>> wrong values as before. I definitely cannot understand why I'm having this
>>>>>> error! It makes no sense....
>>>>>>
>>>>>> 2016-04-18 14:53 GMT+02:00 Laura Joana <laurajoanalopes_at_gmail.com>:
>>>>>>
>>>>>>> Actually I can try to use the compiled version for linux, the same
>>>>>>> as you, and see if my problem goes away...
>>>>>>>
>>>>>>> 2016-04-18 14:52 GMT+02:00 Laura Joana <laurajoanalopes_at_gmail.com>:
>>>>>>>
>>>>>>>> I'm using the same version as you, NAMD 2.11 compiled from source
>>>>>>>> in a linux system, ethernet version! I cannot use the development version
>>>>>>>> because I got some problems with rattle in previous simulations...--94eb2c09e040936ea20530ebc2f5--