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
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Received on Mon Jul 04 2016 - 00:30:02 PDT
