[gmx-users] The trouble with dihedral restraints: frozen peptide backbones

[ms]

On 18/10/10 13:06, Mark Abraham wrote:
> On 18/10/2010 10:53 PM, ms wrote:
>> On 18/10/10 03:30, Mark Abraham wrote:
>>>> To enforce chirality in such a toy, I thought that a simple
>>>> (naive?) but functional idea could be that of enforcing a not-
>>>> too-hard and wide-bottomed dihedral restrain on the phi angle,
>>>> like that:
>>>>
>>>> [ dihedral_restraints ]
>>>> ; ai aj ak
>>>> al type label phi dphi kfac power
>>>> ; phi C'(n-1) - N - CA - C'
>>>> 3
>>>> 5 7 8 1 1 -90 75 2 1
>>>
>>> Try mdrun -debug on a short run. What does it have to say about the
>>> parameter values for this dihedral restraint? Likewise gmxdump -s on
>>> the .tpr (though you will have to search around for F_DIHRES among
>>> other things, probably).
>>>
>>
>> I have run a 500 ps run with -debug on, but I am unsure of where
>> should I look for what it says of relevance -I see the ctab,rtab,dtab
>> xvg's but I doubt they are of interest.
>
> There should be a much larger .log file, probably named differently.
> Check what it reports about dihedral restraints - text searching will be
> your friend, here.
>
> Mark

Thanks a lot. As far as I can see I see an endless amount of the following:

dihres[0]: 2 4 6 7 : phi=-2.239583, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[1]: 7 9 11 12 : phi=-2.264564, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[2]: 12 14 16 17 : phi=-2.286253, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[3]: 17 19 21 22 : phi=-2.285502, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[4]: 22 24 26 27 : phi=-2.325288, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[5]: 27 29 31 32 : phi=-2.333271, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[6]: 32 34 36 37 : phi=-2.344587, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[7]: 37 39 41 42 : phi=-2.359801, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[8]: 42 44 46 47 : phi=-2.347612, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[9]: 47 49 51 52 : phi=-2.375774, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[10]: 52 54 56 57 : phi=-2.370417, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[11]: 57 59 61 62 : phi=-2.385128, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[12]: 62 64 66 67 : phi=-2.411767, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[13]: 67 69 71 72 : phi=-2.383690, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[14]: 72 74 76 77 : phi=-2.444273, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[15]: 77 79 81 82 : phi=-2.391789, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[16]: 82 84 86 87 : phi=-2.416251, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[17]: 87 89 91 92 : phi=-2.419053, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[18]: 92 94 96 97 : phi=-2.441001, dphi=1.308997, kfac=20.000000, 
power=1, label=1
dihres[19]: 97 99 101 102 : phi=-2.437035, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[20]: 102 104 106 107 : phi=-2.405856, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[21]: 107 109 111 112 : phi=-2.430783, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[22]: 112 114 116 117 : phi=-2.405508, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[23]: 117 119 121 122 : phi=-2.386797, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[24]: 122 124 126 127 : phi=-2.388632, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[25]: 127 129 131 132 : phi=-2.419342, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[26]: 132 134 136 137 : phi=-2.396203, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[27]: 137 139 141 142 : phi=-2.409687, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[28]: 142 144 146 147 : phi=-2.372591, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[29]: 147 149 151 152 : phi=-2.376767, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[30]: 152 154 156 157 : phi=-2.355252, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[31]: 157 159 161 162 : phi=-2.356343, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[32]: 162 164 166 167 : phi=-2.344373, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[33]: 167 169 171 172 : phi=-2.337336, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[34]: 172 174 176 177 : phi=-2.299121, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[35]: 177 179 181 182 : phi=-2.294940, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[36]: 182 184 186 187 : phi=-2.297313, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[37]: 187 189 191 192 : phi=-2.287532, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[38]: 192 194 196 197 : phi=-2.255120, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[39]: 197 199 201 202 : phi=-2.221712, dphi=1.308997, 
kfac=20.000000, power=1, label=1
dihres[40]: 202 204 206 207 : phi=-2.115131, dphi=1.308997, 
kfac=20.000000, power=1, label=1

Now, the 1.308997 value stays fixed and seems to be the radiants value 
of the 75 degrees dphi parameter I've put in the topology. The phi 
value, conversely, as it can be seen is not fixed (it changes from angle 
to angle, and from time point to time point) and it's surely not -90 as 
I fixed it (it's about -120 / -140). I strongly suspect however it 
simply reports the radiant *actual* value of the angles during the 
trajectory -but I don't know. kfac=20 makes sense, since I put kfac=2 in 
the topology and dihre_fc=10 in the .mdp.

Should I look for something else in the mdrun0.log ? If you have a fast 
connection, I could put the full dump/log/mdp/whatevers in my web space 
and let you download it, if you can be that nice.

m.