[gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

[Jose Borreguero]

Hi Justin,

​Thanks for your quick reply! ​
This means x2top is not finding
​
or using
the right force constant value, right?
​ I

​
did
 add the bond info into file ffbonded.itp
​of
the oplsa.ff/ directory
​
(https://goo.gl/z5UMot)
.
I also included the types in file
atomtypes.atp
​
 and the non bonded info in
ffnonbonded.itp file. Maybe related to this issue is this line also found
in the output .top file:
​    ​
#include "
​​
./oplsaa.ff/forcefield.itp"
This line should not be necessary because the .top​ file contains all
information. Does the line mean that the bond information in the output
.top file is overridden with that gmx later finds under
​
./oplsaa.ff
​?
​ If so, then the particular value of the force constant in the .top file
would  be irrelevant and my problem would be solved! :)

​.Jose​

​


​.Jose​



On Wed, Jun 21, 2017 at 10:51 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/21/17 10:47 AM, Jose Borreguero wrote:
>
>> Dear Gromacs users,
>>
>> I created the .top file for a small silica crystal that contains only two
>> types of atoms, silicon (type SIO) and oxygen (type OSI). The bond
>> potential is:
>> [ bondtypes ]
>> ; i    j  func       b0          kb
>>    SIO OSI   1
>> ​ ​
>>     0.15783
>> ​   ​
>>    251040
>>
>> After running gmx x2top, the .top file contains
>> [ bonds ]
>> ;  ai    aj funct     c0            c1            c2            c3
>>      1     9     1  1.600000e-01 4.000000e+05  1.600000e-01  4.000000e+05
>>      1    35     1  1.600000e-01 4.000000e+05  1.600000e-01  4.000000e+05
>>
>> I
>> ​assume 0.16 in c0 and c2 is the result of rounding 0.15783, but I ​
>> was expecting number 251040 for c1 and c3, got
>> ​​
>> 400000 instead
>> ​!
>> I don't know the meaning of coefficients c0, c1, c2, and c3
>> ​,​
>> I could not find some explanation for them
>> ​.
>> Can anyone point to a place where these coefficients are described in
>> detail? The description may explain the
>> ​
>> 400000
>> ​ number.
>> ​
>>
>
> It's the default bonded force constant.
>
> gmx help x2top
> "
> ...
>  -kb    <real>   (400000)   Bonded force constant (kJ/mol/nm^2)
> ...
> "
>
> The comment line means little, so there's no specific meaning to c0, c1,
> etc. It generically refers to bonded parameter fields, which for bonds are
> A- and B-state equilibrium lengths and force constants.  For dihedrals
> these mean something entirely different.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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