Re: [gmx-users] v-rescale

2012-09-18 Thread Tsjerk Wassenaar
Hi Sara, NPT also requires a routine for temperature coupling. What makes you wonder about the suitability of v-rescale for that? If you check the mdp files from tutorial stuff, you'll probably encounter the v-rescale method used in the NpT simulations. Cheers, Tsjerk On Sep 18, 2012 7:12 AM, "

[gmx-users] v-rescale

2012-09-18 Thread mohammad agha
Dear Gromacs Users, I have doubt about temperature bath coupling (v-rescale). I use this method (v-rescale) for my system, and my system is NPT ensemble. Has it problem? is v-rescale just used for NVT ensemble or it doesn't have restriction? Please help me. Thank you in advance Best Regards Sar

Res: [gmx-users] V-Rescale Reference

2011-03-03 Thread Ricardo O. S. Soares
Ok, thanks Erik. De: Erik Marklund Para: Discussion list for GROMACS users Cc: Ricardo O. S. Soares Enviadas: Quinta-feira, 3 de Março de 2011 18:58:30 Assunto: Re: [gmx-users] V-Rescale Reference There's a reference in the gromacs manual Ricardo

Re: [gmx-users] V-Rescale Reference

2011-03-03 Thread Erik Marklund
There's a reference in the gromacs manual Ricardo O. S. Soares skrev 2011-03-03 22.52: Dear users, what is the literature reference for using the V-Rescale Thermostat? Maybe the Gromacs 4 paper? Thank you --- Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Departmen

[gmx-users] V-Rescale Reference

2011-03-03 Thread Ricardo O. S. Soares
Dear users, what is the literature reference for using the V-Rescale Thermostat? Maybe the Gromacs 4 paper? Thank you --- Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics & Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of

Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97

2011-01-25 Thread Justin A. Lemkul
= yes gen_temp = 300 gen_seed = 1993 Message: 4 Date: Tue, 25 Jan 2011 08:05:44 -0500 From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> Subject: Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relative

Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97

2011-01-25 Thread Mark Abraham
On 26/01/2011 12:05 AM, Justin A. Lemkul wrote: gromacs wrote: HI Friends, I get the following note, The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. I want to keep the T at 300K, so does it ma

Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97

2011-01-25 Thread Justin A. Lemkul
gromacs wrote: HI Friends, I get the following note, The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. I want to keep the T at 300K, so does it matter to select any thermostat method? The choi

[gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97

2011-01-25 Thread gromacs
HI Friends, I get the following note, The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. I want to keep the T at 300K, so does it matter to select any thermostat method? Another note when i use PME:

RE: [gmx-users] v-rescale and conserved energy

2010-12-01 Thread Berk Hess
ion to the surface tension analytically. Berk From: mstu...@slb.com To: gmx-users@gromacs.org Date: Wed, 1 Dec 2010 12:10:23 + Subject: [gmx-users] v-rescale and conserved energy Dear gromacs users, I am running NVT simulations for polarizable (shell particle) water model (GROMACS version

[gmx-users] v-rescale and conserved energy

2010-12-01 Thread Mikhail Stukan
Dear gromacs users, I am running NVT simulations for polarizable (shell particle) water model (GROMACS version 4.5.1 and 4.5.3 (issue is same in both)) using v-rescale thermostat. While temperature, potential, kinetic and total energies behave quite well I am failing to obtain constant values

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

2009-05-07 Thread Berk Hess
May 2009 14:03:30 +0200 > Subject: [gmx-users] v-rescale - harmonic oscillator > > Hi, > > It is just a diatomic molecule without other interactions (so only > bonded interaction, LJ=0 and charges=0 on the atoms). What other details > would you like to know? Should I send

[gmx-users] v-rescale - harmonic oscillator

2009-05-07 Thread servaas
d energy term? > > > > For very small tau_t the current implementation does not work well. > > Bussi mailed me a proper implementation that I will put in when I have time. > > > > Berk > > > > > From: servaas.michielssens at student.kuleuven.be > &

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

2009-05-07 Thread Berk Hess
-users@gromacs.org > Date: Thu, 7 May 2009 09:02:52 +0200 > Subject: [gmx-users] v-rescale - harmonic oscillator > > Hi, > > I did some experiments with a harmonic oscillator (diatomic molecule > without charge en LJ parameters) using the v-rescale thermostat. First I &g

[gmx-users] v-rescale - harmonic oscillator

2009-05-07 Thread servaas
Hi, I did some experiments with a harmonic oscillator (diatomic molecule without charge en LJ parameters) using the v-rescale thermostat. First I ran a simulation in the NVE ensemble with a time-step of 0.0001ps, total energy was constant here. Then I tried simulating the system with the v-resca