[gmx-users] Re: v-rescale - harmonic oscillator

2009-05-12 Thread Giovanni Bussi
Dear Servaas, the problem that you found is not related to the stochastic rescaling itself, but to the way the effective energy is calculated in gromacs. In particular, the increment in the integral part is not consistent with the applied scaling. You can correct for this by changing

[gmx-users] Re: v-rescale - harmonic oscillator

2009-05-12 Thread servaas
am prepared to help with it or test it if this is required. Kind regards, Servaas - Message: 1 Date: Tue, 12 May 2009 09:06:52 +0200 From: Giovanni Bussi giovanni.bu...@gmail.com Subject: [gmx-users] Re: v-rescale - harmonic oscillator To: gmx-users@gromacs.org

RE: [gmx-users] Re: v-rescale - harmonic oscillator

2009-05-12 Thread Berk Hess
...@student.kuleuven.be To: gmx-users@gromacs.org Date: Tue, 12 May 2009 13:25:02 +0200 Subject: [gmx-users] Re: v-rescale - harmonic oscillator Dear Dr. Bussi, Thank you very much for the explanation of this problem. So I understand that a problem remains with the integrator used

RE: [gmx-users] Re: v-rescale - harmonic oscillator

2009-05-08 Thread Berk Hess
will probably not fix this for 4.0.5, but only for 4.1, so we do not change the reproducibility in minor revisions. Berk From: servaas.michielss...@student.kuleuven.be To: gmx-users@gromacs.org Date: Thu, 7 May 2009 15:27:37 +0200 Subject: [gmx-users] Re: v-rescale - harmonic oscillator Hi Berk

[gmx-users] Re: v-rescale - harmonic oscillator

2009-05-08 Thread servaas
: Berk Hess g...@hotmail.com Subject: RE: [gmx-users] Re: v-rescale - harmonic oscillator To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: col113-w10f68330ea113929cbc3518e...@phx.gbl Content-Type: text/plain; charset=iso-8859-1 Hi, I have come to the conclusion

RE: [gmx-users] Re: v-rescale - harmonic oscillator

2009-05-08 Thread Berk Hess
@gromacs.org Date: Fri, 8 May 2009 11:17:33 +0200 Subject: [gmx-users] Re: v-rescale - harmonic oscillator Hi, Thanks for your confirmation of this problem. One thing is not clear to me from your answer. Has v-rescale fundamental problems with a Harmonic oscillator or is it a problem

RE: [gmx-users] Re: v-rescale - harmonic oscillator

2009-05-07 Thread Berk Hess
Hi, No, only for small values is should be off, maybe tau_t 10 or 100 * delta_t. How did you set up your harmonic oscillator? Berk From: servaas.michielss...@student.kuleuven.be To: gmx-users@gromacs.org Date: Thu, 7 May 2009 12:54:54 +0200 Subject: [gmx-users] Re: v-rescale - harmonic

[gmx-users] Re: v-rescale - harmonic oscillator

2009-05-07 Thread servaas
oscillator? Berk From: servaas.michielss...@student.kuleuven.be To: gmx-users@gromacs.org Date: Thu, 7 May 2009 12:54:54 +0200 Subject: [gmx-users] Re: v-rescale - harmonic oscillator Hi, Thank you for your reply. Yes by effective energy I mean