Re: [gmx-users] SHAKE for water

2013-10-30 Thread Guillaume Chevrot
Hi, 2013/10/30 Justin Lemkul > > > On 10/30/13 12:00 PM, Guillaume Chevrot wrote: > >> Hi, >> >> I was wondering if there is an option or a way to use the algorithm SHAKE >> for the water molecules (instead of SETTLE). >> >> > Never t

[gmx-users] SHAKE for water

2013-10-30 Thread Guillaume Chevrot
Hi, I was wondering if there is an option or a way to use the algorithm SHAKE for the water molecules (instead of SETTLE). Thanks! Guillaume -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-25 Thread Guillaume Chevrot
Note that using md-vv guarantees the 2007 paper is inapplicable, because > > GROMACS did not have a velocity Verlet integrator back then. Sharing the > > .log files might be informative. > > > > Mark > > > > > > On Fri, Oct 11, 2013 at 11:38 PM, Guillaume

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-12 Thread Guillaume Chevrot
LE. > > > > Note that using md-vv guarantees the 2007 paper is inapplicable, because > > GROMACS did not have a velocity Verlet integrator back then. Sharing the > > .log files might be informative. > > > > Mark > > > > > > On Fri, Oct 11, 2013 a

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-12 Thread Guillaume Chevrot
. > .log files might be informative. > > Here is the link where you can find the log file: http://dx.doi.org/10.6084/m9.figshare.821211 Thanks for your comments! Guillaume > Mark > > > On Fri, Oct 11, 2013 at 11:38 PM, Guillaume Chevrot < > guillaume.chev...@gmail

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-11 Thread Guillaume Chevrot
not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 2013/10/11 Mark Abraham > On Oct 11, 2013 7:59 PM, "Guillaume Chevrot" > wrote: > > > > Hi all, >

[gmx-users] energy drift - comparison of double and single precision

2013-10-11 Thread Guillaume Chevrot
Hi all, I recently compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision lysozyme in water / NVE ensemble / double precision ... and what I found was quite ... disturbing (see the attached figure - plots of the total energy). I observe a constant drift in

[gmx-users] Re: Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1

2013-08-09 Thread Guillaume Chevrot
Hi, I just did the simulation with the last version of Gromacs (4.6.3) and it seems that the problem has disappeared!! Regards, Guillaume -- View this message in context: http://gromacs.5086.x6.nabble.com/Mean-Square-Displacement-gromacs-4-5-Vs-gromacs-4-6-1-tp5010317p5010425.html Sent from

[gmx-users] Re: Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1

2013-08-04 Thread Guillaume Chevrot
Hi, I effectively refer to the MSD of the protein. My simulation is different compared to the simulation of a lipid bilayer and the "normal" MSD for a protein in water should be equivalent to the red plot. I forgot to mention but the MSD are obtained from 10 ns NVE simulations. Regards, Guill

[gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1

2013-08-02 Thread Guillaume Chevrot
Hi, I performed 2 simulations of a lysozyme in water: one with the version 4.5 of Gromacs and another with the version 4.6.1 (I used the exact same inputs). Then I calculated the MSD and I obtained a complete different behavior with the version 4.6.1 of Gromacs and this MSD is obviously wrong. <