From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jan 18 2018 - 06:50:07 CST
You need to make a cleared distinction between the chemical role of
hydrogen bond acceptors vs. the way that these are treated in the force
field.
If you don't have explicit acceptor groups, the cause of a failed
minimization is unlikely to come from there.
Giacomo
On Thu, Jan 18, 2018 at 12:48 AM, Suresh Ghimire <
suresh.ghimire2049sg_at_gmail.com> wrote:
> Yes, as I am new to nanotube and its psf file. First I looked at the psf
> file given on permeation of water through nanotube, there I found nonzero
> acceptors but
> 0 !NACC: acceptors on my new psf file developed by using nanotube plug-in
> of VMD and having the problem in minimizing the energy. Is there any effect
> of zero accepters on minimization?
>
> On Wed, Jan 17, 2018 at 10:05 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com
> > wrote:
>
>> Do you mean the following donor and acceptor PSF fields? Those
>> correspond to very old terms of the CHARMM potential that are not used any
>> more, because the combination of partial charges and Lennard-Jones
>> coefficients allows to reproduce hydrogen bonds already. Without reading
>> corresponding terms in the parameter file, I believe that explicit
>> donor-acceptor pairs will be ignored. But you should definitely verify
>> that by checking the energy at the first timestep.
>>
>> 0 !NDON: donors
>>
>>
>> 0 !NACC: acceptors
>>
>>
>> On Wed, Jan 17, 2018 at 1:02 AM, Suresh Ghimire <
>> suresh.ghimire2049sg_at_gmail.com> wrote:
>>
>>>
>>> Dear namd user,
>>> I have prepared psf file for nanotube and water system. In my psf file
>>> there is zero accepter but there are non zero acceptors on psf file of the
>>> tutorial. Is it necessary to have non zero acceptors?
>>>
>>> --
>>> Regards
>>> Suresh Ghimire
>>> M Sc (Physics)
>>> Tribhuvan University, Patan Multiple Campus
>>> Lalitpur, Nepal
>>>
>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>
>
> --
> Regards
> Suresh Ghimire
> M Sc (Physics)
> Tribhuvan University, Patan Multiple Campus
> Lalitpur, Nepal
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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