Re: [gmx-users] Freezing groups and energy conservation

I am running in single precision, my time-step is 1 fs (0.001 ps, usually works fine). However, I achieved very good energy conservation when I changed integrator from md to md-vv. It sounds quite strange to me, but it works, so... Thanks, however! Francesco -- Gromacs Users mailing list *

[gmx-users] Freezing groups and energy conservation

alternatives to do that? In fact also position restraints cause to me a negative energy drift, in this case. Thanks Francesco Mambretti, LCP, University of Milan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] Meaningless pressure values: NVT and NVE ensembles

coupling, potential has a cutoff and it is shifted to 0 in correspondence of cutoff radius. Thanks, Francesco Mambretti -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org

Re: [gmx-users] Meaningless pressure values: NVT and NVE ensembles

Thanks for the suggestion, but I fear it is not my case. I obtain the same meaningless results with version 5.0.2 installed on another pc of my university. I suspect it is something in Gromacs procedure for computing pressures. However, thanks Francesco -- Gromacs Users mailing list *

Re: [gmx-users] Meaningless pressure values: NVT and NVE ensembles

So you confirm me that pressure calculation in Gromacs is done through virial theorem and should provide meaningful results? I start from a perfect fcc crystal and launch simulations of 20 ps...is it a too short simulation? density and temperature should be already optimized for argon solid

Re: [gmx-users] Meaningless pressure values: NVT and NVE ensembles

Statistics over 501 steps [ 0. through 5000. ps ], 5 data sets All statistics are over 5001 points Energy Average Err.Est. RMSD Tot-Drift --- Potential -8.01936

Re: [gmx-users] Meaningless pressure values: NVT and NVE ensembles

Sure! here it is. Am I missing anything? Thanks ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 500 ; mode for center of mass motion removal comm-mode

[gmx-users] R: Tabulated potentials

I forgot to add that I start from a liquid system and that my simulation is run in microcanonical system at a temperature well below the melting point for argon. Francesco Mambretti Il 03/11/14 11:57, Francesco Mambretti francesco.mambre...@studenti.unimi.it ha scritto: Dear GROMACS

[gmx-users] Tabulated potentials

the two cases is the use of a tabulated interaction instead that LJ GROMACS default. Do you know anything about similar problems with freeze groups? Thanks a lot Francesco Mambretti -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

[gmx-users] Static structure factor

it? It is just the Fourier transform of g(r) or it is calculated directly as rho (q) rho (-q)? 2) In the latter case, how can I get the static structure factor separately for the three cartesian axis? Thanks in advance, Francesco Mambretti, LCP (Parallel Computing Laboratory, University of Milan

[gmx-users] User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2

user-defined potentials with verlet's cutoff? This would be a serious handicap for this code! Am I forced to use charge groups? Thanks in advance, Francesco Mambretti - University of Milan - LCP (Parallel Computing Lab) -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] R: Re: User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2

version, so that I am not forced to use verlet cutoff if I want a configuration that scales fast 3) use LJ potential Am I right? Francesco Il 02/10/14, Mark Abraham mark.j.abra...@gmail.com ha scritto: On Thu, Oct 2, 2014 at 11:58 AM, Francesco Mambretti francesco.mambre...@studenti.unimi.it

[gmx-users] R: Re: R: Re: User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2

Abraham mark.j.abra...@gmail.com ha scritto: On Thu, Oct 2, 2014 at 1:13 PM, Francesco Mambretti francesco.mambre...@studenti.unimi.it wrote: So then, you have to update the pages on your website ( http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential