Nilesh Dhumal wrote:
Hello Justin,
I used 0.1fs timestep and I could get dielectric constant around 56 which
looks ok. To get the dielectric constant around ~75, should I reduce the
timestep around 0.05fs.
I have no idea. Try it.
I used temperature 298k for my simulation and average tmep
Hello Justin,
I used 0.1fs timestep and I could get dielectric constant around 56 which
looks ok. To get the dielectric constant around ~75, should I reduce the
timestep around 0.05fs.
I used temperature 298k for my simulation and average tmep. I got is
297.83 K. I am doing NPT and used 1.0 bar a
Nilesh Dhumal wrote:
I have general question. If this parameters are not giving the proper
results then How come I get the proper results with same parameter if I
use 1/2 value of Kbond with the same parameters.
Random chance, I imagine. Your .mdp settings are not correct and the cutoffs
a
I have general question. If this parameters are not giving the proper
results then How come I get the proper results with same parameter if I
use 1/2 value of Kbond with the same parameters.
I checked the temp when I use half value of Kbond and it goes max. ~320.
Nilesh
On Wed, May 11, 2011 4:03
Nilesh Dhumal wrote:
Hello Justin,
I used 0.5 fs time step and still I got dielectric constant ~2.
This is the md.mdp file I used. I checked the temperature it didn't go
more than ~ 320 K.
Still, that's unacceptable if your ref_t is 295. The fact that the temperature
is still rocketing
Hello Justin,
I used 0.5 fs time step and still I got dielectric constant ~2.
This is the md.mdp file I used. I checked the temperature it didn't go
more than ~ 320 K.
title = cpeptide MD
cpp = /usr/bin/cpp
integrator = md
dt = 0.001
The gmx-developers list is not the forum for these types of questions. I am
replying via gmx-users, which is where the discussion should stay.
I took a few minutes to dig into this. My conclusion is that your system is not
stable. I would encourage you to analyze the temperature and pressu
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