Hi Nisha,I did not try OPLSAA since I need TIP3P model with CHARMM. With this FF hydrogens are also considered as interaction sites. This is not very good combination for GROMACS, but it appeared that the differences are not too big and the time required for simulation with H interacttion side is s
Hi Zuzana,
You are right. I did get my density to ~0.986g/cm3, and I
actually came across this other paper by Price and Brooks, and
initially they get a density of Tip3p using pme at around 0.979g/cm3,
but they tweak some of the parameters in oplsaa to get the correct
density. I am n
Hi Nisha,I have performed a benchmark simulations of TIP3P water and I still obtained density 0.984g.cm-3. It looks that this model gives such a density. If you look at JCP 79, 926, 1983 you will see that the authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo other properties, each mo
On 1/04/2010 4:58 AM, nishap.pa...@utoronto.ca wrote:
Hello,
So I looked at the manual and I changed my mdp parameters as follows to
equilibrate at a constant pressure.
RUN CONTROL PARAMETERS =
integrator = sd
tinit = 0
dt = 0.002
nsteps = 50
nstcomm = 1
nstxout = 0
nstvout = 0
nstfout = 0
Hello,
So I looked at the manual and I changed my mdp parameters as
follows to equilibrate at a constant pressure.
RUN CONTROL PARAMETERS =
integrator = sd
tinit= 0
dt = 0.002
nsteps = 50
nstcomm
Thanks. I will look up the manual again.
Quoting Sander Pronk :
Hi Nisha,
Looking at your .mdp, there are some issues that might lead to the
behavior that you describe:
First: you should try to look up the published densities for tip3p
water at 300K - they might actually be close to what
Hi Nisha,
Looking at your .mdp, there are some issues that might lead to the behavior
that you describe:
First: you should try to look up the published densities for tip3p water at
300K - they might actually be close to what you get.
Second: your neighbor list cut-off (rlist) might be too small
I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density
when I create the box using genbox is 997.177g/l. I did energy
minimization run and the potential energy did converge smoothly, so I
did NPT equilibration run of 100ps and I got the density value of
975g/l. Why does the de
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