[gmx-users] buckingham potentials

[sreelakshmi ramesh]

I am using gromos force field fotr my work and This force field's
files come filled
 with LJ  functions and now if i want to work with buckingham
potential i changed in
default section of force field ffG34a21.itp file but it gives me the
follwing errors

ERROR 77 [file ffgmxnb.itp, line 144]:
  Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)

any help appreciated.


On Wed, Dec 22, 2010 at 8:40 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> sreelakshmi ramesh wrote:
>
>>
>> so if i set vdwtype =cut off and specify 2 in default section (2 is for
>> buck and 1 for LJ ) of topology file will gromacs makes suer that i want the
>> calculation with bucking ham potential.
>>
>
> Presumably, since that's what the manual would indicate works.  You can
> answer these sorts of questions yourself by giving it a try, then verifying
> the run parameters by using gmxdump on the resulting .tpr file.
>
> -Justin
>
>  On Wed, Dec 22, 2010 at 8:32 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    sreelakshmi ramesh wrote:
>>
>>        Thanks a lot for timely reply by gmxusers.I read the manual and
>>        i had altered the buckingham coefficients in topolgy file.Now in
>>        mdp file in vdwtype i want to specify it as buckingham but looks
>>        like i can mention only LJ and in manual they haven't told about
>>        the notation for BJ.any suggestions please.
>>
>>
>>    Use of Buckingham potentials is not controlled by the .mdp file,
>>    except in the fact that several of the vdwtype methods cannot be
>>    used in conjunction with Buckingham (see manual, section 7.3.11);
>>    only "cutoff" appears to be viable here.
>>
>>    -Justin
>>
>>
>>        sree.
>>
>>
>>        On Tue, Dec 21, 2010 at 6:02 PM, Justin A. Lemkul
>>        <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>        <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>>
>>
>>
>>           sreelakshmi ramesh wrote:
>>
>>               can anyone tell me how to alter the parameter B OF
>> buckingham
>>               potential.
>>
>>
>>           Manual, chapter 5, especially table 5.4, which specifically
>> lists
>>           all of the parameters and where they are defined.
>>
>>           -Justin
>>
>>               regards,
>>               sree
>>
>>
>>           --     ========================================
>>
>>           Justin A. Lemkul
>>           Ph.D. Candidate
>>           ICTAS Doctoral Scholar
>>           MILES-IGERT Trainee
>>           Department of Biochemistry
>>           Virginia Tech
>>           Blacksburg, VA
>>           jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>>
>>        231-9080
>>
>>           http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>           ========================================
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>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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