[gmx-users] Re: Re: swiss param query

case where there is only one protein chain and no ions in your PDB file (the topol.top file looks different). Enjoy, Michel On 12 oct. 10, at 14:28, gmx-users-requ...@gromacs.org wrote: From: Michel Cuendet Date: 12 octobre 2010 13:09:22 HAE (ÉUA) To: gmx-users@gromacs.org Subject: [gmx

Re: [gmx-users] Re: swiss param query

) and hence skip the chimera step. I just submitted a molecule but haven't got the result yet, is there an off-line version? Or one where I can send 200 molecules? ====== Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinfo

[gmx-users] Re: swiss param query

ram == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne Switzerland http://lausanne.isb-sib.ch/~mcuendet/ == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/ma

[gmx-users] SwissParam

for such a procedure. Enjoy SwissParam, and please notify us of any question or suggestion for improvement. Try SwissParam now !! Best regards, Michel Cuendet ====== Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformati

Re: [gmx-users] g_sas, what's it all about?

nberg seems more detailed though, because it attributes different weights to surface patches depending on the type of the underlying atom. It would be interesting to know why this method has not been more widely used. Best, Michel -- ========== Michel

[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling

quot; than the NH? Both thermostats have to impose the same (canonical) temperature fluctuations on the system, pumping heat in and out (in case the uncoupled dynamics were really conservative). I still need to read the Bussi et al. paper, though. Cheers, Michel =

Re: [gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling

ion even in a non-equilibrium case. Sorry for the long email :) Michel -- ========== Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland http:/

[gmx-users] trjcat -cat skips frames

ritten was 15431, time 300.00 ps === ========== Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland

[gmx-users] g_hbond -contact -xpm does not work

Hi, I'm trying to look at contacts between two proteins at the individual atom level. I have a bunch of analysis scripts that use the .xpm file and work for h-bonds, so I wanted to use the output of g_hbond 3.3.2 again with the option -contact. But: g_hbond -hbn -hbm -num -contact -r 0.4 g

Re: [gmx-users] g-hbond and N acceptors

ot to do this.) -- ====== Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == ___ gmx-users mailing list

[gmx-users] g-hbond and N acceptors

ehavior of g_hbond been modified in later versions of gromacs regarding the N- acceptor behavior ? Thanks, Michel ====== Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne S

[gmx-users] Re: mdrun -rerun and box size bug not fixed?

y doing some testing: (a) Do some reprocessing with PME rather than RF to see if that helps. (b) Do some reprocessing on full precision trajectories rather than xtcs to rule out precision issues etc. Best wishes, David ========== Michel Cuendet, Ph

[gmx-users] Re: mdrun -rerun and box size bug not fixed?

pe of recovering better energies with a rerun? Thanks, Michel Original Message Subject:Re: mdrun -rerun and box size bug not fixed? Date: Tue, 06 Nov 2007 14:12:29 +0100 From: Michel Cuendet <[EMAIL PROTECTED]> To: gmx-users@gromacs.org References: <[EMAIL P

[gmx-users] Re: mdrun -rerun and box size bug not fixed?

1 the averages are wrong in md.log and at the end of the run. Bye, Michel == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne Switze

[gmx-users] Re: mdrun -rerun and box size bug not fixed?

nstenergy = 1 NO rescaling of velocities NO rescaling of box size Do read the box sizes from the trajectory Cheers, Michel ====== Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerla

[gmx-users] Re: mdrun -rerun and box size bug not fixed?

energies that I'm missing it. Anyway, hopefully (a) is true, otherwise I'm going to need to repeat a LOT of work (and be very grumpy). Keep me posted on this. Thanks, David -- ====== Michel Cuendet, Ph.D Molecular Modeling Group Sw

[gmx-users] Re: mdrun -rerun and box size bug not fixed?

ery grumpy). Keep me posted on this. Thanks, David ====== Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == __

[gmx-users] mdrun 3.3.2 crash - gmx_sumi called in serial run with RF

not with cutoff on the electrostatics. I ran the gmxtest suite, and the error appears in ./gmxtest/complex/acetonitrilRF, which is also the only testcase unsing reaction field... Cheers, M -- == Michel Cuendet, Ph.D Molecular Modeling

[gmx-users] mdrun -rerun and box size bug not fixed?

like me trying to use the -rerun option... Thanks, Michel -- ====== Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecul