From: Ashutosh Shandilya (scfbioiitd_at_gmail.com)
Date: Wed Nov 17 2021 - 13:08:38 CST
I increased harmonic restrain to 5.0 using command
abf {
colvars gs
fullSamples 1000
historyfreq 100000
hidejacobian off
}
harmonic {
colvars gs
centers 0.0
forceconstant 5.0
}
Output file shows the same RMSD for all the structures something like this
which should not be the case. Is it because i switched off
*usesecondclosestframe* off. I have been trying to change several
parameters in the input but still getting some kind of error.
Frame index: 67 ; optimal RMSD = 0.985712
Frame index: 80 ; optimal RMSD = 0.985712
Frame index: 79 ; optimal RMSD = 0.985712
Frame index: 78 ; optimal RMSD = 0.985712
Frame index: 77 ; optimal RMSD = 0.985712
Frame index: 76 ; optimal RMSD = 0.985712
Frame index: 75 ; optimal RMSD = 0.985712
Frame index: 74 ; optimal RMSD = 0.985712
Frame index: 73 ; optimal RMSD = 0.985712
Frame index: 72 ; optimal RMSD = 0.985712
Frame index: 71 ; optimal RMSD = 0.985712
Frame index: 70 ; optimal RMSD = 0.985712
Frame index: 69 ; optimal RMSD = 0.985712
Frame index: 68 ; optimal RMSD = 0.985712
Frame index: 81 ; optimal RMSD = 0.985712
Frame index: 66 ; optimal RMSD = 0.985712
Frame index: 65 ; optimal RMSD = 0.985712
Frame index: 64 ; optimal RMSD = 0.985712
Frame index: 63 ; optimal RMSD = 0.985712
Frame index: 62 ; optimal RMSD = 0.985712
Frame index: 61 ; optimal RMSD = 0.985712
Frame index: 60 ; optimal RMSD = 0.985712
Frame index: 59 ; optimal RMSD = 0.985712
Frame index: 58 ; optimal RMSD = 0.985712
Frame index: 57 ; optimal RMSD = 0.985712
Frame index: 56 ; optimal RMSD = 0.985712
Frame index: 55 ; optimal RMSD = 0.985712
Frame index: 94 ; optimal RMSD = 0.985712
Frame index: 107 ; optimal RMSD = 0.985712
108 PDB structures were obtained from the PNEB path. I computed RMSD with
VMD which is mentioned below. Kindly have a look and suggest. My actual
RMSD varies like this.
1 0.5520958304405212
2 0.6408998370170593
3 0.7004873752593994
4 0.7478375434875488
5 0.7849769592285156
6 0.8124300241470337
7 0.829501748085022
8 0.8617943525314331
9 0.8889437317848206
10 0.9140389561653137
11 0.925011396408081
12 0.931750476360321
13 0.9490005373954773
14 0.9639561176300049
15 0.9865623712539673
16 1.0129530429840088
17 1.017659068107605
18 1.0304405689239502
19 1.05254328250885
20 1.0523943901062012
21 1.0497472286224365
22 1.0674532651901245
23 1.0869779586791992
24 1.1080254316329956
25 1.1066851615905762
26 1.1148474216461182
27 1.1117987632751465
28 1.1251643896102905
29 1.1315655708312988
30 1.1351579427719116
31 1.1500359773635864
32 1.1598128080368042
33 1.1690787076950073
34 1.1832456588745117
35 1.190578579902649
36 1.1949034929275513
37 1.2126442193984985
38 1.2073010206222534
39 1.2080799341201782
40 1.2127560377120972
41 1.2220537662506104
42 1.2297075986862183
43 1.2463030815124512
44 1.258796215057373
45 1.2574396133422852
46 1.2649439573287964
Kindly suggest.
Thanks,
Ashutosh
On Wed, Nov 17, 2021 at 1:32 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> There *were* multiple RMSD computations, because that's how the distances
> between path frames are computed.
>
> You are also omitting several warnings above, btw. One was "Please check
> your configuration or increase restraint on z(σ)". What did you do there?
>
> I don't know where you got the PDB structures from, but I recommend that
> you load them in VMD and compute the RMSD of the coordinates of your
> simulation with respect to each. All RMSDs need to be well defined in
> order to be able to compute the path variable derived from them.
>
> Giacomo
>
>
> On Wed, Nov 17, 2021 at 12:55 PM Ashutosh Shandilya <scfbioiitd_at_gmail.com>
> wrote:
>
>> Thanks for your reply, As I understand I should consider the selection
>> which has only moderate change. First step itself gives this problem so I
>> have not calculated the RMSD. I have a string of pdbs from PNEB path and I
>> want to have a pmf that's why I am using abf. So the selected atoms have
>> lots of transformation. So what are the options.
>>
>> Many thanks,
>> Ashutosh
>>
>> On Wed, Nov 17, 2021 at 11:28 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>> wrote:
>>
>>> This message is the key:
>>> colvars: This is usually the result of an ill-defined set of atoms for
>>> rotational alignment (RMSD, rotateReference, etc).
>>>
>>> If the structure of the group of atoms changes too much, it becomes
>>> possible that a pure rotation is not the transformation that minimizes the
>>> RMSD, but another transformation does (e.g. rotation + reflection across a
>>> plane).
>>>
>>> You do not need to change the time step, but instead pick a selection
>>> that is guaranteed to have only moderate changes in structure. Practically
>>> speaking, the RMSD should remain much lower than the radius of gyration--000000000000aa525805d100d26a--
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