Hello guys,
Any feedback ? Is this a known problem
or just an artifact due to my simulation environment.
If so, please let me know where I am committing the mistake.
I have shared the files via above mentioned link.
Has anybody done lipid14 simulation while restraining atoms
with harmonic potential?
Thank you for your consideration.
On Mon, Jul 4, 2016 at 12:46 PM Himanshu Joshi <himanshuphy87.gmail.com>
wrote:
> Hello amberits,
> I am running a POPC simulation *(**lipid14 FF*) using* pmemd.MPI *in
> *amber14 *. While equilibrating the membrane in *npt,* I am harmonically
> restraining the solute *(1Kcal/mol)* with *ntr=1.* But the density is
> not converging to 1 rather it always maintains below 1 (0. 85) even after 3
> ns of simulation. Also, the distribution of water molecules in the box is
> not uniform. I am sharing the input files and output files of the
> simulation through the following dropbox link. The output files also
> contain the trajectory of the simulation (hold_3.nc) with 30 frames.
>
> https://www.dropbox.com/sh/zy7l5fd2pnm2cba/AABAVWcNCOgT3HFyNCvzbalxa?dl=0
>
> I suspect it has to do something with* nscm* since if I don't use ntr=1,
> the density goes to 1 in 20 ps and water box is also fine.
> Any comment or suggestion is highly appreciated.
>
> P>S> I had reported a similar issue in the second part of the following
> discussion upto some extent, I sincerely apologize for talking about this
> after so long.
> http://archive.ambermd.org/201511/0231.html
>
> --
> With Regards
> Himanshu Joshi
> Department of Physics
> IISc Bangalore India
> 560012
>
--
With Regards
Himanshu Joshi
Department of Physics
IISc Bangalore India
560012
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Received on Sat Jul 09 2016 - 13:00:03 PDT
