[gmx-users] Dihedral Restrain Syntax 4.6

[Johnny Lu]

Thank you very much for clarifying this. I was looking all over the web for
half a day.

One last question on this topic:
Does the dihedral constraint specified in this way involve any
time/ensemble averaging?


On Thu, Aug 14, 2014 at 10:10 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/14/14, 10:02 AM, Johnny Lu wrote:
>
>> I forget to mention that in the alanine dipeptide topol.top that I made, I
>> tried:
>> [ dihedral_restraints ]
>>    12 11 13 15 1 1 90 0 2000.0 1
>> #endif
>>
>> but,
>> Program grompp, VERSION 4.6.5
>> Source code file: /build/buildd/gromacs-4.6.5/src/kernel/toppush.c, line:
>> 1914
>>
>> Fatal error:
>> Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest..
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
> Manual section 4.3.3 and Table 5.5 allude to the proper usage, though
> admittedly I see that Table 5.5 is incorrect, as it is missing the value of
> k.
>
> Going into the code, the proper syntax is to specify the four atoms to be
> restrained and phi, dphi, k as the 3 parameters that the fatal error
> suggests. I don't know what function type to set, probably just 1.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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