Actually I want to run an qmmm run with gaussian in no PBC condition in the
NVT ensemble and under a spherical potential.
On Thu, Aug 1, 2024 at 4:36 PM Carlos Simmerling <
carlos.simmerling.stonybrook.edu> wrote:
> I don't think Amber has support for such a simulation, but you could make
> changes to the source code.
>
> maybe if you can explain what you are trying to achieve we could suggest
> other ways to do it.
>
> On Thu, Aug 1, 2024 at 5:55 AM Dulal Mondal <
> babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
>
>> Thank you sir for your reply. At first I ran NVT equilibration with cubic
>> box and with PBC. (ntb=1, ntt=3,gamma_ln=1.0).
>>
>> Then I strip the solvent water using parmed beyond 15 angstrom to
>> generate prmtop and inpcrd file. Now, I have a spherical system with no box
>> information. Then I want to equilibrate this spherical system with no PBC
>> condition and NVT ensemble.
>>
>> On Thu, Aug 1, 2024 at 3:14 PM Carlos Simmerling <
>> carlos.simmerling.stonybrook.edu> wrote:
>>
>>> No this is not correct. If the box is off (ntb=0) there is no defined
>>> volume so it is not NVT. Why do you want constant volume but not periodic
>>> interactions?
>>>
>>>
>>> On Thu, Aug 1, 2024, 2:20 AM Dulal Mondal via AMBER <amber.ambermd.org>
>>> wrote:
>>>
>>>> Dear Experts,
>>>> I am trying to generate a production run input file in the following
>>>> condition.
>>>> 1) Non-bonded interactions including the van der Waals interaction are
>>>> just
>>>> truncated at cutoff distance. PME (Particle mesh Ewald) is off.
>>>> 2) No PBC ( Non-boundary condition).
>>>> 3) NVT ensemble.
>>>>
>>>> My mdin file is like below.
>>>> equilibrating in NVT
>>>> &cntrl
>>>> imin=0,
>>>> irest=1,
>>>> ntx=5,
>>>> *ntb=0, # no periodicity is applied and PME is off *
>>>>
>>>> * ntt=3,gamma_ln=1.0, tempi=300.0,temp0=300.0, # NVT ensemble*
>>>> nstlim=1000,dt=0.001,
>>>> ntpr=5,ntwx=5,ntwr=5,
>>>> ifqnt=1,
>>>> cut=8.0,
>>>>
>>>> Is my mdin file correct?
>>>> --
>>>> *With regards,*
>>>> *Dulal Mondal,*
>>>> *Research Scholar,*
>>>> *Department of Chemistry,*
>>>> *IIT Kharagpur, Kharagpur 721302.*
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>
>> --
>> *With regards,*
>> *Dulal Mondal,*
>> *Research Scholar,*
>> *Department of Chemistry,*
>> *IIT Kharagpur, Kharagpur 721302.*
>>
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Thu Aug 01 2024 - 05:30:02 PDT
