Hi, David;
Thank you so much for your prompt response. Your answer is really helpful.
On Mon, Apr 20, 2009 at 10:31 PM, David van der Spoel
wrote:
> Yanmei Song wrote:
>>
>> Hi, David:
>>
>> I performed the NEMD and got the following results for averaging the
>> last 1 ns. So the second column
Yanmei Song wrote:
Hi, David:
I performed the NEMD and got the following results for averaging the
last 1 ns. So the second column should be the acceleration and last
column should be the 1/viscosity. But notice that there are so many
big negative numbers, which makes the average negative. C
Hi, David:
I performed the NEMD and got the following results for averaging the
last 1 ns. So the second column should be the acceleration and last
column should be the 1/viscosity. But notice that there are so many
big negative numbers, which makes the average negative. Can you help
me out he
Yanmei Song wrote:
Yes, I want to get the equilibrium viscosity. My question is how I can
identify the system approach a zero acceleration after I try several
values. Thank you so much for your help.
Plot viscosity as a function of acceleration. Check the reference
(Wensink et al.) that I mailed
Yes, I want to get the equilibrium viscosity. My question is how I can
identify the system approach a zero acceleration after I try several
values. Thank you so much for your help.
On Mon, Apr 20, 2009 at 10:17 AM, David van der Spoel
wrote:
> Yanmei Song wrote:
>>
>> Dear David:
>>
>> Thank you
Yanmei Song wrote:
Dear David:
Thank you for your answer. i still have several questions.
Do I have to start the non-equilibrium simulation after the system
reach the equilibrium? Or I just need to start at the same starting
point as the my equilibrium systems?
At least equilibrium density.
Dear David:
Thank you for your answer. i still have several questions.
Do I have to start the non-equilibrium simulation after the system
reach the equilibrium? Or I just need to start at the same starting
point as the my equilibrium systems?
What I need to do is just add the cos_acceleration: t
Yanmei Song wrote:
Dear All:
I wanted to get the viscosity of my simulated polymer system. From the
manual it said that : GROMACS also has a non-equilibrium method for
determining the viscosity" (page 123) Does this mean I just need to do
a separate non-equilibrium MD run? In terms of mdp file,
Dear All:
I wanted to get the viscosity of my simulated polymer system. From the
manual it said that : GROMACS also has a non-equilibrium method for
determining the viscosity" (page 123) Does this mean I just need to do
a separate non-equilibrium MD run? In terms of mdp file, I just need
to add th
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