[gmx-users] A question on Berendsen NVT ensemble
lzheng at me.rochester.edu
Tue Apr 30 20:42:30 CEST 2002
Thanks, David. The density is about 2.2g/cm^3(1536 atoms in a cubic of a
length of 2.866nm.) I found that the initial pressure is very high
(~10^10Pa). Is it also due to the high density?
On Tue, 30 Apr 2002, David van der Spoel wrote:
>On Tue, 30 Apr 2002, Lianqing Zheng wrote:
>>This is a problem on Berendsen NVT ensemble which appeared in my MD code.
>>I found the equilibrium temperature is dependent on parameter Tao_T: the
>>larger Tao_T, the higher the final temperature the system reaches. For
>>example, the T I expect the system to reach is 7000K, however it reaches
>>10000K when Tao_T is 0.1ps, 7200K when Tao_T=0.01ps, 7100K when
>>Tao_T=0.005ps. The time step is 0.001ps.
>>Do you have any insight on what's going wrong with my code?
>You must have very repulsive forces. Have you checked the pressure? Most
>likely you are simulating at too high a density (for the model)
>Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
>Husargatan 3, Box 576, 75123 Uppsala, Sweden
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