Re: Re: [gmx-users] Nose-hoover T-coupling in REMD

2011-01-09 Thread wibke . sudholt
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Re: [gmx-users] Nose-hoover T-coupling in REMD

2011-01-09 Thread Qin Qiao
2010/12/26 ms deviceran...@gmail.com On 25/12/10 02:12, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? As far as

Re: [gmx-users] Nose-hoover T-coupling in REMD

2010-12-25 Thread ms
On 25/12/10 02:12, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? As far as I know v-rescale should generate a correct

Re: [gmx-users] Nose-hoover T-coupling in REMD

2010-12-25 Thread Qin Qiao
I'm not sure, since actually kinetic energy should have fluctuation, and the v-rescaling may suppress the fluctuation.. 2010/12/25 ms deviceran...@gmail.com On 25/12/10 02:12, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's

Re: [gmx-users] Nose-hoover T-coupling in REMD

2010-12-25 Thread Mark Abraham
On 25/12/2010 1:12 PM, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? I'm quite curious how to choose the frequency of

Re: [gmx-users] Nose-hoover T-coupling in REMD

2010-12-25 Thread ms
On 25/12/10 02:12, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? As far as I know v-rescale should generate a correct

Re: [gmx-users] Nose-hoover T-coupling in REMD

2010-12-24 Thread Mark Abraham
On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong temperature coupling to make sure every replica

Re: [gmx-users] Nose-hoover T-coupling in REMD

2010-12-24 Thread David van der Spoel
On 2010-12-24 11.04, Mark Abraham wrote: On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong

Re: [gmx-users] Nose-hoover T-coupling in REMD

2010-12-24 Thread ms
On 24/12/10 10:36, David van der Spoel wrote: On 2010-12-24 11.04, Mark Abraham wrote: On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm

Re: [gmx-users] Nose-hoover T-coupling in REMD

2010-12-24 Thread David van der Spoel
On 2010-12-24 13.15, ms wrote: On 24/12/10 10:36, David van der Spoel wrote: On 2010-12-24 11.04, Mark Abraham wrote: On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope

Re: [gmx-users] Nose-hoover T-coupling in REMD

2010-12-24 Thread ms
On 24/12/10 12:26, David van der Spoel wrote: I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. V-rescale

Re: [gmx-users] Nose-hoover T-coupling in REMD

2010-12-24 Thread David van der Spoel
On 12/24/10 6:40 PM, ms wrote: On 24/12/10 12:26, David van der Spoel wrote: I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the

Re: [gmx-users] Nose-hoover T-coupling in REMD

2010-12-24 Thread Qin Qiao
Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? I'm quite curious how to choose the frequency of the T-coupling in REMD. Though it seems the