Hi. Thanks for the reply. So you are saying that the topology file should look
more like:
[bonds]
; ai aj funct c0 c1 c2 c3
1 2 9 1
1 3 9 1
1 4 9 1
1 5 9 1
5 6 9 1
5 7 9 1
5 15 9 1
assuming the table file is called table_b1.xvg???
And then I should just run it using
mdrun -v -tableb table_b1.xvg -deffnm run>& ./output0
On Nov 30, 2012, at 2:21 PM, Berk Hess wrote:
>
>
>
> ----------------------------------------
>> Date: Thu, 29 Nov 2012 08:58:50 -0500
>> From: [email protected]
>> To: [email protected]
>> Subject: Re: [gmx-users] Electrostatic field in atoms - GROMACS is not
>> reading table interaction functions for bonded interactions
>>
>>
>>
>> On 11/29/12 8:18 AM, Ariana Torres Knoop wrote:
>>> Dear GROMACS users,
>>>
>>> We are trying to determine the electric fields at the C and N atoms in a
>>> protein. To do so, we thought of performing a one step energy minimization
>>> with the Lennard-Jones as well as the bonded interactions turned off, in
>>> order to get only the coulomb forces.
>>> For that, according to
>>> www.gromacs.org/Documentation/How-tos/Tabulated_Potentials , we made a
>>> table (table.xvg) in which the Lennard-Jones potential was set to zero and
>>> we also made three tables (table_b1.xvg, table_a5.xvg and table_d5.xvg)
>>> according to section 4.2.13 of the Manual (Tabulated interaction
>>> functions), in which the f(x)=0 for the whole range of distances, angles,
>>> dihedrals present in the simulation box. The numbers 1, 5, 2 correspond to
>>> the function number referred to in the topology file. For example for the
>>> bonds interaction, in the topology file we have:
>>> [ bonds ]
>>> ; ai aj funct c0 c1 c2 c3
>>> 1 2 1
>>> 1 3 1
>>> 1 4 1
>>> 1 5 1
>>> 5 6 1
>>> .
>>> .
>>> .
>>> so we named the table "table_b1.xvg".
>>>
>>> We changed the run.mdp file as follows:
>>> vdw-type = User
>>> coulombtype = PME-User
>>>
>>> And then we try to run it using:
>>> mdrun -v -deffnm run.tpr
>>>
>>> When checking the energy contribution using g_energy, Lennard-Jones
>>> contribution was indeed zero, but
>>> for the bonded interactions this is not the case:
>>>
>>> Energy Average Err.Est. RMSD Tot-Drift
>>> -------------------------------------------------------------------------------
>>> U-B 18180.1 -- 276.416 -540.638 (kJ/mol)
>>> Proper Dih. 11732.3 -- 27.6829 -54.0396 (kJ/mol)
>>> Improper Dih. 1027.26 -- 47.1598 -91.7097 (kJ/mol)
>>> LJ-14 0 -- 0 0 (kJ/mol)
>>> LJ (SR) 0 -- 0 0 (kJ/mol)
>>>
>>> We though that maybe the tables for the bonded interactions were not taken,
>>> so we tried:
>>> mdrun -v -tableb table_b1.xvg table_a5.xvg table_d2.xvg -deffnm run.tpr
>>>
>>> But it also did not work.
>>>
>>> We are not sure whether the problem is in the table definition, the way of
>>> running the program, the run type, the name of the tables, or if there
>>> should be some other modifications in the *mdp file.
>>>
>>> We would be very grateful if anyone could help us out here.
>>>
>>
>> I think the problem comes from the fact that the function types you are
>> specifying in the topology correspond to actual potentials and thus the
>> tables
>> are being ignored. Per Table 5.5, it seems that any value for the table is
>> acceptable (n >= 0) but using numbers corresponding to actual function types
>> may
>> not work. The specified format also requires that both the table number and
>> force constant (k) be specified in the topology, but the [bonds] section you
>> show above has no value of k and the function type corresponds to a simple
>> harmonic bond. There is no "bond" energy in the output, which suggests you
>> are
>> using constraints - is that the case?
>
> No, the issue is that you are using function type 1. Tabulated bonds are
> function type 8 or 9,
> that is what should be in the 3rd column.
> The actual number for the table file should appear after that in the 4th
> column.
>
> Cheers,
>
> Berk
>
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
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