Tip4pew and most water models are intended to be used with shake.
On Wed, Sep 6, 2023, 2:43 AM Zafar,Muhammad Saqlain via AMBER <
amber.ambermd.org> wrote:
> Hello,
>
> i do not use SHAKE algorithm.
>
> I got my starting structure by the following script. I have also attach my
> tip4pew.pdb starting file.
>
> source leaprc.water.tip4pew
> loadamberparams frcmod.tip4pew
> saveamberparm TP4 tip4pew.parm7 tip4pew.rst7
> quit
>
> cpptraj
> parm tip4pew.parm7
> trajin tip4pew.rst7
> trajout tip4pew.pdb include_ep
>
>
>
>
> ________________________________
> 보낸 사람: David A Case <dacase1.gmail.com>
> 보낸 날짜: 2023년 9월 6일 수요일 오전 7:56
> 받는 사람: Zafar,Muhammad Saqlain <saqlainzafar.gm.gist.ac.kr>; AMBER Mailing
> List <amber.ambermd.org>
> 제목: Re: [AMBER] Problem with water molecules angle in MD simulation
>
> On Tue, Sep 05, 2023, Zafar,Muhammad Saqlain via AMBER wrote:
> >
> >I am using TIP4P/EW water model for simulation of pure water system.
> >
> >In start the angle that i notice in my pdb is around 104, but when i
> >run NPT for 100ns on TIP4P/ew water model the pdb file that i got after
> >simulation done the average angle of my system is around 99.
> >
> >How to resolve this issue or is it normal in using amber.
>
> TIP4P/Ew is a rigid water model, so the angles should never change. Are
> you
> always using SHAKE when running these simulations? Every water should have
> exactly the same H-O-H angle.
>
> Since we don't know where you starting structure came from, there is not
> much we can say about what to expect it's water geometry to look like.
>
> ...dac
>
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Received on Wed Sep 06 2023 - 02:30:02 PDT
